Efficient similarity computations on parallel machines using data shaping

Similarity computation is a fundamental operation in all forms of data. Big Data is, typically, characterized by attributes such as volume, velocity, variety, veracity, etc. In general, Big Data variety appears as structured, semi-structured or unstructured forms. The volume of Big Data in general, and semi-structured data in particular, is increasing at a phenomenal rate. Big Data phenomenon is posing new set of challenges to similarity computation problems occurring in semi-structured data. Technology and processor architecture trends suggest very strongly that future processors shall have ten\u27s of thousands of cores (hardware threads). Another crucial trend is that ratio between on-chip and off-chip memory to core counts is decreasing. State-of-the-art parallel computing platforms such as General Purpose Graphics Processors (GPUs) and MICs are promising for high performance as well high throughput computing. However, processing semi-structured component of Big Data efficiently using parallel computing systems (e.g. GPUs) is challenging. Reason being most of the emerging platforms (e.g. GPUs) are organized as Single Instruction Multiple Thread/Data machines which are highly structured, where several cores (streaming processors) operate in lock-step manner, or they require a high degree of task-level parallelism. We argue that effective and efficient solutions to key similarity computation problems need to operate in a synergistic manner with the underlying computing hardware. Moreover, semi-structured form input data needs to be shaped or reorganized with the goal to exploit the enormous computing power of \textit{state-of-the-art} highly threaded architectures such as GPUs. For example, shaping input data (via encoding) with minimal data-dependence can facilitate flexible and concurrent computations on high throughput accelerators/co-processors such as GPU, MIC, etc. We consider various instances of traditional and futuristic problems occurring in intersection of semi-structured data and data analytics. Preprocessing is an operation common at initial stages of data processing pipelines. Typically, the preprocessing involves operations such as data extraction, data selection, etc. In context of semi-structured data, twig filtering is used in identifying (and extracting) data of interest. Duplicate detection and record linkage operations are useful in preprocessing tasks such as data cleaning, data fusion, and also useful in data mining, etc., in order to find similar tree objects. Likewise, tree edit is a fundamental metric used in context of tree problems; and similarity computation between trees another key problem in context of Big Data. This dissertation makes a case for platform-centric data shaping as a potent mechanism to tackle the data- and architecture-borne issues in context of semi-structured data processing on GPU and GPU-like parallel architecture machines. In this dissertation, we propose several data shaping techniques for tree matching problems occurring in semi-structured data. We experiment with real world datasets. The experimental results obtained reveal that the proposed platform-centric data shaping approach is effective for computing similarities between tree objects using GPGPUs. The techniques proposed result in performance gains up to three orders of magnitude, subject to problem and platform

Data De-Duplication in NoSQL Databases

With the popularity and expansion of Cloud Computing, NoSQL databases (DBs) are becoming the preferred choice of storing data in the Cloud. Because they are highly de-normalized, these DBs tend to store significant amounts of redundant data. Data de-duplication (DD) has an important role in reducing storage consumption to make it affordable to manage in today’s explosive data growth. Numerous DD methodologies like chunking and, delta encoding are available today to optimize the use of storage. These technologies approach DD at file and/or sub-file level but this approach has never been optimal for NoSQL DBs. This research proposes data De-Duplication in NoSQL Databases (DDNSDB) which makes use of a DD approach at a higher level of abstraction, namely at the DB level. It makes use of the structural information about the data (metadata) exploiting its granularity to identify and remove duplicates. The main goals of this research are: to maximally reduce the amount of duplicates in one type of NoSQL DBs, namely the key-value store, to maximally increase the process performance such that the backup window is marginally affected, and to design with horizontal scaling in mind such that it would run on a Cloud Platform competitively. Additionally, this research presents an analysis of the various types of NoSQL DBs (such as key-value, tabular/columnar, and document DBs) to understand their data model required for the design and implementation of DDNSDB. Primary experiments have demonstrated that DDNSDB can further reduce the NoSQL DB storage space compared with current archiving methods (from 17% to near 69% as more structural information is available). Also, by following an optimized adapted MapReduce architecture, DDNSDB proves to have competitive performance advantage in a horizontal scaling cloud environment compared with a vertical scaling environment (from 28.8 milliseconds to 34.9 milliseconds as the number of parallel Virtual Machines grows)

Design and implementation of a multi-agent opportunistic grid computing platform

Opportunistic Grid Computing involves joining idle computing resources in enterprises into a converged high performance commodity infrastructure. The research described in this dissertation investigates the viability of public resource computing in offering a plethora of possibilities through seamless access to shared compute and storage resources. The research proposes and conceptualizes the Multi-Agent Opportunistic Grid (MAOG) solution in an Information and Communication Technologies for Development (ICT4D) initiative to address some limitations prevalent in traditional distributed system implementations. Proof-of-concept software components based on JADE (Java Agent Development Framework) validated Multi-Agent Systems (MAS) as an important tool for provisioning of Opportunistic Grid Computing platforms. Exploration of agent technologies within the research context identified two key components which improve access to extended computer capabilities. The first component is a Mobile Agent (MA) compute component in which a group of agents interact to pool shared processor cycles. The compute component integrates dynamic resource identification and allocation strategies by incorporating the Contract Net Protocol (CNP) and rule based reasoning concepts. The second service is a MAS based storage component realized through disk mirroring and Google file-system’s chunking with atomic append storage techniques. This research provides a candidate Opportunistic Grid Computing platform design and implementation through the use of MAS. Experiments conducted validated the design and implementation of the compute and storage services. From results, support for processing user applications; resource identification and allocation; and rule based reasoning validated the MA compute component. A MAS based file-system that implements chunking optimizations was considered to be optimum based on evaluations. The findings from the undertaken experiments also validated the functional adequacy of the implementation, and show the suitability of MAS for provisioning of robust, autonomous, and intelligent platforms. The context of this research, ICT4D, provides a solution to optimizing and increasing the utilization of computing resources that are usually idle in these contexts

Improving Data Management and Data Movement Efficiency in Hybrid Storage Systems

University of Minnesota Ph.D. dissertation.July 2017. Major: Computer Science. Advisor: David Du. 1 computer file (PDF); ix, 116 pages.In the big data era, large volumes of data being continuously generated drive the emergence of high performance large capacity storage systems. To reduce the total cost of ownership, storage systems are built in a more composite way with many different types of emerging storage technologies/devices including Storage Class Memory (SCM), Solid State Drives (SSD), Shingle Magnetic Recording (SMR), Hard Disk Drives (HDD), and even across off-premise cloud storage. To make better utilization of each type of storage, industries have provided multi-tier storage through dynamically placing hot data in the faster tiers and cold data in the slower tiers. Data movement happens between devices on one single device and as well as between devices connected via various networks. Toward improving data management and data movement efficiency in such hybrid storage systems, this work makes the following contributions: To bridge the giant semantic gap between applications and modern storage systems, passing a piece of tiny and useful information (I/O access hints) from upper layers to the block storage layer may greatly improve application performance or ease data management in heterogeneous storage systems. We present and develop a generic and flexible framework, called HintStor, to execute and evaluate various I/O access hints on heterogeneous storage systems with minor modifications to the kernel and applications. The design of HintStor contains a new application/user level interface, a file system plugin and a block storage data manager. With HintStor, storage systems composed of various storage devices can perform pre-devised data placement, space reallocation and data migration polices assisted by the added access hints. Each storage device/technology has its own unique price-performance tradeoffs and idiosyncrasies with respect to workload characteristics they prefer to support. To explore the internal access patterns and thus efficiently place data on storage systems with fully connected (i.e., data can move from one device to any other device instead of moving tier by tier) differential pools (each pool consists of storage devices of a particular type), we propose a chunk-level storage-aware workload analyzer framework, simplified as ChewAnalyzer. With ChewAnalzyer, the storage manager can adequately distribute and move the data chunks across different storage pools. To reduce the duplicate content transferred between local storage devices and devices in remote data centers, an inline Network Redundancy Elimination (NRE) process with Content-Defined Chunking (CDC) policy can obtain a higher Redundancy Elimination (RE) ratio but may suffer from a considerably higher computational requirement than fixed-size chunking. We build an inline NRE appliance which incorporates an improved FPGA based scheme to speed up CDC processing. To efficiently utilize the hardware resources, the whole NRE process is handled by a Virtualized NRE (VNRE) controller. The uniqueness of this VNRE that we developed lies in its ability to exploit the redundancy patterns of different TCP flows and customize the chunking process to achieve a higher RE ratio

TailoredRE: A Personalized Cloud-based Traffic Redundancy Elimination for Smartphones

The exceptional rise in usages of mobile devices such as smartphones and tablets has contributed to a massive increase in wireless network trac both Cellular (3G/4G/LTE) and WiFi. The unprecedented growth in wireless network trac not only strain the battery of the mobile devices but also bogs down the last-hop wireless access links. Interestingly, a signicant part of this data trac exhibits high level of redundancy in them due to repeated access of popular contents in the web. Hence, a good amount of research both in academia and in industries has studied, analyzed and designed diverse systems that attempt to eliminate redundancy in the network trac. Several of the existing Trac Redundancy Elimination (TRE) solutions either does not improve last-hop wireless access links or involves inecient use of compute resources from resource-constrained mobile devices. In this research, we propose TailoredRE, a personalized cloud-based trac redundancy elimination system. The main objective of TailoredRE is to tailor TRE mechanism such that TRE is performed against selected applications rather than application agnostically, thus improving eciency by avoiding caching of unnecessary data chunks. In our system, we leverage the rich resources of the cloud to conduct TRE by ooading most of the operational cost from the smartphones or mobile devices to its clones (proxies) available in the cloud. We cluster the multiple individual user clones in the cloud based on the factors of connectedness among users such as usage of similar applications, common interests in specic web contents etc., to improve the eciency of caching in the cloud. This thesis encompasses motivation, system design along with detailed analysis of the results obtained through simulation and real implementation of TailoredRE system

Design and implementation of a multi-agent opportunistic grid computing platform

Opportunistic Grid Computing involves joining idle computing resources in enterprises into a converged high performance commodity infrastructure. The research described in this dissertation investigates the viability of public resource computing in offering a plethora of possibilities through seamless access to shared compute and storage resources. The research proposes and conceptualizes the Multi-Agent Opportunistic Grid (MAOG) solution in an Information and Communication Technologies for Development (ICT4D) initiative to address some limitations prevalent in traditional distributed system implementations. Proof-of-concept software components based on JADE (Java Agent Development Framework) validated Multi-Agent Systems (MAS) as an important tool for provisioning of Opportunistic Grid Computing platforms. Exploration of agent technologies within the research context identified two key components which improve access to extended computer capabilities. The first component is a Mobile Agent (MA) compute component in which a group of agents interact to pool shared processor cycles. The compute component integrates dynamic resource identification and allocation strategies by incorporating the Contract Net Protocol (CNP) and rule based reasoning concepts. The second service is a MAS based storage component realized through disk mirroring and Google file-system’s chunking with atomic append storage techniques. This research provides a candidate Opportunistic Grid Computing platform design and implementation through the use of MAS. Experiments conducted validated the design and implementation of the compute and storage services. From results, support for processing user applications; resource identification and allocation; and rule based reasoning validated the MA compute component. A MAS based file-system that implements chunking optimizations was considered to be optimum based on evaluations. The findings from the undertaken experiments also validated the functional adequacy of the implementation, and show the suitability of MAS for provisioning of robust, autonomous, and intelligent platforms. The context of this research, ICT4D, provides a solution to optimizing and increasing the utilization of computing resources that are usually idle in these contexts

The 1995 Science Information Management and Data Compression Workshop

This document is the proceedings from the 'Science Information Management and Data Compression Workshop,' which was held on October 26-27, 1995, at the NASA Goddard Space Flight Center, Greenbelt, Maryland. The Workshop explored promising computational approaches for handling the collection, ingestion, archival, and retrieval of large quantities of data in future Earth and space science missions. It consisted of fourteen presentations covering a range of information management and data compression approaches that are being or have been integrated into actual or prototypical Earth or space science data information systems, or that hold promise for such an application. The Workshop was organized by James C. Tilton and Robert F. Cromp of the NASA Goddard Space Flight Center

Doctor of Philosophy

dissertationAs the base of the software stack, system-level software is expected to provide ecient and scalable storage, communication, security and resource management functionalities. However, there are many computationally expensive functionalities at the system level, such as encryption, packet inspection, and error correction. All of these require substantial computing power. What's more, today's application workloads have entered gigabyte and terabyte scales, which demand even more computing power. To solve the rapidly increased computing power demand at the system level, this dissertation proposes using parallel graphics pro- cessing units (GPUs) in system software. GPUs excel at parallel computing, and also have a much faster development trend in parallel performance than central processing units (CPUs). However, system-level software has been originally designed to be latency-oriented. GPUs are designed for long-running computation and large-scale data processing, which are throughput-oriented. Such mismatch makes it dicult to t the system-level software with the GPUs. This dissertation presents generic principles of system-level GPU computing developed during the process of creating our two general frameworks for integrating GPU computing in storage and network packet processing. The principles are generic design techniques and abstractions to deal with common system-level GPU computing challenges. Those principles have been evaluated in concrete cases including storage and network packet processing applications that have been augmented with GPU computing. The signicant performance improvement found in the evaluation shows the eectiveness and eciency of the proposed techniques and abstractions. This dissertation also presents a literature survey of the relatively young system-level GPU computing area, to introduce the state of the art in both applications and techniques, and also their future potentials

Personal Data Management in the Internet of Things

Due to a sharp decrease in hardware costs and shrinking form factors, networked sensors have become ubiquitous. Today, a variety of sensors are embedded into smartphones, tablets, and personal wearable devices, and are commonly installed in homes and buildings. Sensors are used to collect data about people in their proximity, referred to as users. The collection of such networked sensors is commonly referred to as the Internet of Things. Although sensor data enables a wide range of applications from security, to efficiency, to healthcare, this data can be used to reveal unwarranted private information about users. Thus it is imperative to preserve data privacy while providing users with a wide variety of applications to process their personal data. Unfortunately, most existing systems do not meet these goals. Users are either forced to release their data to third parties, such as application developers, thus giving up data privacy in exchange for using data-driven applications, or are limited to using a fixed set of applications, such as those provided by the sensor manufacturer. To avoid this trade-off, users may chose to host their data and applications on their personal devices, but this requires them to maintain data backups and ensure application performance. What is needed, therefore, is a system that gives users flexibility in their choice of data-driven applications while preserving their data privacy, without burdening users with the need to backup their data and providing computational resources for their applications. We propose a software architecture that leverages a user's personal virtual execution environment (VEE) to host data-driven applications. This dissertation describes key software techniques and mechanisms that are necessary to enable this architecture. First, we provide a proof-of-concept implementation of our proposed architecture and demonstrate a privacy-preserving ecosystem of applications that process users' energy data as a case study. Second, we present a data management system (called Bolt) that provides applications with efficient storage and retrieval of time-series data, and guarantees the confidentiality and integrity of stored data. We then present a methodology to provision large numbers of personal VEEs on a single physical machine, and demonstrate its use with LinuX Containers (LXC). We conclude by outlining the design of an abstract framework to allow users to balance data privacy and application utility