AT-GIS: highly parallel spatial query processing with associative transducers

Users in many domains, including urban planning, transportation, and environmental science want to execute analytical queries over continuously updated spatial datasets. Current solutions for largescale spatial query processing either rely on extensions to RDBMS, which entails expensive loading and indexing phases when the data changes, or distributed map/reduce frameworks, running on resource-hungry compute clusters. Both solutions struggle with the sequential bottleneck of parsing complex, hierarchical spatial data formats, which frequently dominates query execution time. Our goal is to fully exploit the parallelism offered by modern multicore CPUs for parsing and query execution, thus providing the performance of a cluster with the resources of a single machine. We describe AT-GIS, a highly-parallel spatial query processing system that scales linearly to a large number of CPU cores. ATGIS integrates the parsing and querying of spatial data using a new computational abstraction called associative transducers(ATs). ATs can form a single data-parallel pipeline for computation without requiring the spatial input data to be split into logically independent blocks. Using ATs, AT-GIS can execute, in parallel, spatial query operators on the raw input data in multiple formats, without any pre-processing. On a single 64-core machine, AT-GIS provides 3× the performance of an 8-node Hadoop cluster with 192 cores for containment queries, and 10× for aggregation queries

Distance Range Queries in SpatialHadoop

Efficient processing of Distance Range Queries (DRQs) is of great importance in spatial databases due to the wide area of applications. This type of spatial query is characterized by a distance range over one or two datasets. The most representative and known DRQs are the ε Distance Range Query (εDRQ) and the ε Distance Range Join Query (εDRJQ). Given the increasing volume of spatial data, it is difficult to perform a DRQ on a centralized machine efficiently. Moreover, the εDRJQ is an expensive spatial operation, since it can be considered a combination of the εDR and the spatial join queries. For this reason, this paper addresses the problem of computing DRQs on big spatial datasets in SpatialHadoop, an extension of Hadoop that supports spatial operations efficiently, and proposes new algorithms in SpatialHadoop to perform efficient parallel DRQs on large-scale spatial datasets. We have evaluated the performance of the proposed algorithms in several situations with big synthetic and real-world datasets. The experiments have demonstrated the efficiency and scalability of our proposal

CoPart: a context-based partitioning technique for big data

The MapReduce programming paradigm is frequently used in order to process and analyse a huge amount of data. This paradigm relies on the ability to apply the same operation in parallel on independent chunks of data. The consequence is that the overall performances greatly depend on the way data are partitioned among the various computation nodes. The default partitioning technique, provided by systems like Hadoop or Spark, basically performs a random subdivision of the input records, without considering the nature and correlation between them. Even if such approach can be appropriate in the simplest case where all the input records have to be always analyzed, it becomes a limit for sophisticated analyses, in which correlations between records can be exploited to preliminarily prune unnecessary computations. In this paper we design a context-based multi-dimensional partitioning technique, called COPART, which takes care of data correlation in order to determine how records are subdivided between splits (i.e., units of work assigned to a computation node). More specifically, it considers not only the correlation of data w.r.t. contextual attributes, but also the distribution of each contextual dimension in the dataset. We experimentally compare our approach with existing ones, considering both quality criteria and the query execution times

A design space for RDF data representations

RDF triplestores' ability to store and query knowledge bases augmented with semantic annotations has attracted the attention of both research and industry. A multitude of systems offer varying data representation and indexing schemes. However, as recently shown for designing data structures, many design choices are biased by outdated considerations and may not result in the most efficient data representation for a given query workload. To overcome this limitation, we identify a novel three-dimensional design space. Within this design space, we map the trade-offs between different RDF data representations employed as part of an RDF triplestore and identify unexplored solutions. We complement the review with an empirical evaluation of ten standard SPARQL benchmarks to examine the prevalence of these access patterns in synthetic and real query workloads. We find some access patterns, to be both prevalent in the workloads and under-supported by existing triplestores. This shows the capabilities of our model to be used by RDF store designers to reason about different design choices and allow a (possibly artificially intelligent) designer to evaluate the fit between a given system design and a query workload

Online Integration of Semistructured Data

Data integration systems play an important role in the development of distributed multi-database systems. Data integration collects data from heterogeneous and distributed sources, and provides a global view of data to the users. Systems need to process user\u27s applications in the shortest possible time. The virtualization approach to data integration systems ensures that the answers to user requests are the most up-to-date ones. In contrast, the materialization approach reduces data transmission time at the expense of data consistency between the central and remote sites. The virtualization approach to data integration systems can be applied in either batch or online mode. Batch processing requires all data to be available at a central site before processing is started. Delays in transmission of data over a network contribute to a longer processing time. On the other hand, in an online processing mode data integration is performed piece-by-piece as soon as a unit of data is available at the central site. An online processing mode presents the partial results to the users earlier. Due to the heterogeneity of data models at the remote sites, a semistructured global view of data is required. The performance of data integration systems depends on an appropriate data model and the appropriate data integration algorithms used. This thesis presents a new algorithm for immediate processing of data collected from remote and autonomous database systems. The algorithm utilizes the idle processing states while the central site waits for completion of data transmission to produce instant partial results. A decomposition strategy included in the algorithm balances of the computations between the central and remote sites to force maximum resource utilization at both sites. The thesis chooses the XML data model for the representation of semistructured data, and presents a new formalization of the XML data model together with a set of algebraic operations. The XML data model is used to provide a virtual global view of semistructured data. The algebraic operators are consistent with operations of relational algebra, such that any existing syntax based query optimization technique developed for the relational model of data can be directly applied. The thesis shows how to optimize online processing by generating one online integration plan for several data increments. Further, the thesis shows how each independent increment expression can be processed in a parallel mode on a multi core processor system. The dynamic scheduling system proposed in the thesis is able to defer or terminate a plan such that materialization updates and unnecessary computations are minimized. The thesis shows that processing data chunks of fragmented XML documents allows for data integration in a shorter period of time. Finally, the thesis provides a clear formalization of the semistructured data model, a set of algorithms with high-level descriptions, and running examples. These formal backgrounds show that the proposed algorithms are implementable

Efficient processing of large-scale spatio-temporal data

Millionen Geräte, wie z.B. Mobiltelefone, Autos und Umweltsensoren senden ihre Positionen zusammen mit einem Zeitstempel und weiteren Nutzdaten an einen Server zu verschiedenen Analysezwecken. Die Positionsinformationen und übertragenen Ereignisinformationen werden als Punkte oder Polygone dargestellt. Eine weitere Art räumlicher Daten sind Rasterdaten, die zum Beispiel von Kameras und Sensoren produziert werden. Diese großen räumlich-zeitlichen Datenmengen können nur auf skalierbaren Plattformen wie Hadoop und Apache Spark verarbeitet werden, die jedoch z.B. die Nachbarschaftsinformation nicht ausnutzen können - was die Ausführung bestimmter Anfragen praktisch unmöglich macht. Die wiederholten Ausführungen der Analyseprogramme während ihrer Entwicklung und durch verschiedene Nutzer resultieren in langen Ausführungszeiten und hohen Kosten für gemietete Ressourcen, die durch die Wiederverwendung von Zwischenergebnissen reduziert werden können. Diese Arbeit beschäftigt sich mit den beiden oben beschriebenen Herausforderungen. Wir präsentieren zunächst das STARK Framework für die Verarbeitung räumlich-zeitlicher Vektor- und Rasterdaten in Apache Spark. Wir identifizieren verschiedene Algorithmen für Operatoren und analysieren, wie diese von den Eigenschaften der zugrundeliegenden Plattform profitieren können. Weiterhin wird untersucht, wie Indexe in der verteilten und parallelen Umgebung realisiert werden können. Außerdem vergleichen wir Partitionierungsmethoden, die unterschiedlich gut mit ungleichmäßiger Datenverteilung und der Größe der Datenmenge umgehen können und präsentieren einen Ansatz um die auf Operatorebene zu verarbeitende Datenmenge frühzeitig zu reduzieren. Um die Ausführungszeit von Programmen zu verkürzen, stellen wir einen Ansatz zur transparenten Materialisierung von Zwischenergebnissen vor. Dieser Ansatz benutzt ein Entscheidungsmodell, welches auf den tatsächlichen Operatorkosten basiert. In der Evaluierung vergleichen wir die verschiedenen Implementierungs- sowie Konfigurationsmöglichkeiten in STARK und identifizieren Szenarien wann Partitionierung und Indexierung eingesetzt werden sollten. Außerdem vergleichen wir STARK mit verwandten Systemen. Im zweiten Teil der Evaluierung zeigen wir, dass die transparente Wiederverwendung der materialisierten Zwischenergebnisse die Ausführungszeit der Programme signifikant verringern kann.Millions of location-aware devices, such as mobile phones, cars, and environmental sensors constantly report their positions often in combination with a timestamp to a server for different kinds of analyses. While the location information of the devices and reported events is represented as points and polygons, raster data is another type of spatial data, which is for example produced by cameras and sensors. This Big spatio-temporal Data needs to be processed on scalable platforms, such as Hadoop and Apache Spark, which, however, are unaware of, e.g., spatial neighborhood, what makes them practically impossible to use for this kind of data. The repeated executions of the programs during development and by different users result in long execution times and potentially high costs in rented clusters, which can be reduced by reusing commonly computed intermediate results. Within this thesis, we tackle the two challenges described above. First, we present the STARK framework for processing spatio-temporal vector and raster data on the Apache Spark stack. For operators, we identify several possible algorithms and study how they can benefit from the underlying platform's properties. We further investigate how indexes can be realized in the distributed and parallel architecture of Big Data processing engines and compare methods for data partitioning, which perform differently well with respect to data skew and data set size. Furthermore, an approach to reduce the amount of data to process at operator level is presented. In order to reduce the execution times, we introduce an approach to transparently recycle intermediate results of dataflow programs, based on operator costs. To compute the costs, we instrument the programs with profiling code to gather the execution time and result size of the operators. In the evaluation, we first compare the various implementation and configuration possibilities in STARK and identify scenarios when and how partitioning and indexing should be applied. We further compare STARK to related systems and show that we can achieve significantly better execution times, not only when exploiting existing partitioning information. In the second part of the evaluation, we show that with the transparent cost-based materialization and recycling of intermediate results, the execution times of programs can be reduced significantly

Resiliency Mechanisms for In-Memory Column Stores

The key objective of database systems is to reliably manage data, while high query throughput and low query latency are core requirements. To date, database research activities mostly concentrated on the second part. However, due to the constant shrinking of transistor feature sizes, integrated circuits become more and more unreliable and transient hardware errors in the form of multi-bit flips become more and more prominent. In a more recent study (2013), in a large high-performance cluster with around 8500 nodes, a failure rate of 40 FIT per DRAM device was measured. For their system, this means that every 10 hours there occurs a single- or multi-bit flip, which is unacceptably high for enterprise and HPC scenarios. Causes can be cosmic rays, heat, or electrical crosstalk, with the latter being exploited actively through the RowHammer attack. It was shown that memory cells are more prone to bit flips than logic gates and several surveys found multi-bit flip events in main memory modules of today's data centers. Due to the shift towards in-memory data management systems, where all business related data and query intermediate results are kept solely in fast main memory, such systems are in great danger to deliver corrupt results to their users. Hardware techniques can not be scaled to compensate the exponentially increasing error rates. In other domains, there is an increasing interest in software-based solutions to this problem, but these proposed methods come along with huge runtime and/or storage overheads. These are unacceptable for in-memory data management systems. In this thesis, we investigate how to integrate bit flip detection mechanisms into in-memory data management systems. To achieve this goal, we first build an understanding of bit flip detection techniques and select two error codes, AN codes and XOR checksums, suitable to the requirements of in-memory data management systems. The most important requirement is effectiveness of the codes to detect bit flips. We meet this goal through AN codes, which exhibit better and adaptable error detection capabilities than those found in today's hardware. The second most important goal is efficiency in terms of coding latency. We meet this by introducing a fundamental performance improvements to AN codes, and by vectorizing both chosen codes' operations. We integrate bit flip detection mechanisms into the lowest storage layer and the query processing layer in such a way that the remaining data management system and the user can stay oblivious of any error detection. This includes both base columns and pointer-heavy index structures such as the ubiquitous B-Tree. Additionally, our approach allows adaptable, on-the-fly bit flip detection during query processing, with only very little impact on query latency. AN coding allows to recode intermediate results with virtually no performance penalty. We support our claims by providing exhaustive runtime and throughput measurements throughout the whole thesis and with an end-to-end evaluation using the Star Schema Benchmark. To the best of our knowledge, we are the first to present such holistic and fast bit flip detection in a large software infrastructure such as in-memory data management systems. Finally, most of the source code fragments used to obtain the results in this thesis are open source and freely available.:1 INTRODUCTION 1.1 Contributions of this Thesis 1.2 Outline 2 PROBLEM DESCRIPTION AND RELATED WORK 2.1 Reliable Data Management on Reliable Hardware 2.2 The Shift Towards Unreliable Hardware 2.3 Hardware-Based Mitigation of Bit Flips 2.4 Data Management System Requirements 2.5 Software-Based Techniques For Handling Bit Flips 2.5.1 Operating System-Level Techniques 2.5.2 Compiler-Level Techniques 2.5.3 Application-Level Techniques 2.6 Summary and Conclusions 3 ANALYSIS OF CODING TECHNIQUES 3.1 Selection of Error Codes 3.1.1 Hamming Coding 3.1.2 XOR Checksums 3.1.3 AN Coding 3.1.4 Summary and Conclusions 3.2 Probabilities of Silent Data Corruption 3.2.1 Probabilities of Hamming Codes 3.2.2 Probabilities of XOR Checksums 3.2.3 Probabilities of AN Codes 3.2.4 Concrete Error Models 3.2.5 Summary and Conclusions 3.3 Throughput Considerations 3.3.1 Test Systems Descriptions 3.3.2 Vectorizing Hamming Coding 3.3.3 Vectorizing XOR Checksums 3.3.4 Vectorizing AN Coding 3.3.5 Summary and Conclusions 3.4 Comparison of Error Codes 3.4.1 Effectiveness 3.4.2 Efficiency 3.4.3 Runtime Adaptability 3.5 Performance Optimizations for AN Coding 3.5.1 The Modular Multiplicative Inverse 3.5.2 Faster Softening 3.5.3 Faster Error Detection 3.5.4 Comparison to Original AN Coding 3.5.5 The Multiplicative Inverse Anomaly 3.6 Summary 4 BIT FLIP DETECTING STORAGE 4.1 Column Store Architecture 4.1.1 Logical Data Types 4.1.2 Storage Model 4.1.3 Data Representation 4.1.4 Data Layout 4.1.5 Tree Index Structures 4.1.6 Summary 4.2 Hardened Data Storage 4.2.1 Hardened Physical Data Types 4.2.2 Hardened Lightweight Compression 4.2.3 Hardened Data Layout 4.2.4 UDI Operations 4.2.5 Summary and Conclusions 4.3 Hardened Tree Index Structures 4.3.1 B-Tree Verification Techniques 4.3.2 Justification For Further Techniques 4.3.3 The Error Detecting B-Tree 4.4 Summary 5 BIT FLIP DETECTING QUERY PROCESSING 5.1 Column Store Query Processing 5.2 Bit Flip Detection Opportunities 5.2.1 Early Onetime Detection 5.2.2 Late Onetime Detection 5.2.3 Continuous Detection 5.2.4 Miscellaneous Processing Aspects 5.2.5 Summary and Conclusions 5.3 Hardened Intermediate Results 5.3.1 Materialization of Hardened Intermediates 5.3.2 Hardened Bitmaps 5.4 Summary 6 END-TO-END EVALUATION 6.1 Prototype Implementation 6.1.1 AHEAD Architecture 6.1.2 Diversity of Physical Operators 6.1.3 One Concrete Operator Realization 6.1.4 Summary and Conclusions 6.2 Performance of Individual Operators 6.2.1 Selection on One Predicate 6.2.2 Selection on Two Predicates 6.2.3 Join Operators 6.2.4 Grouping and Aggregation 6.2.5 Delta Operator 6.2.6 Summary and Conclusions 6.3 Star Schema Benchmark Queries 6.3.1 Query Runtimes 6.3.2 Improvements Through Vectorization 6.3.3 Storage Overhead 6.3.4 Summary and Conclusions 6.4 Error Detecting B-Tree 6.4.1 Single Key Lookup 6.4.2 Key Value-Pair Insertion 6.5 Summary 7 SUMMARY AND CONCLUSIONS 7.1 Future Work A APPENDIX A.1 List of Golden As A.2 More on Hamming Coding A.2.1 Code examples A.2.2 Vectorization BIBLIOGRAPHY LIST OF FIGURES LIST OF TABLES LIST OF LISTINGS LIST OF ACRONYMS LIST OF SYMBOLS LIST OF DEFINITION

Data Infrastructure for Medical Research

While we are witnessing rapid growth in data across the sciences and in many applications, this growth is particularly remarkable in the medical domain, be it because of higher resolution instruments and diagnostic tools (e.g. MRI), new sources of structured data like activity trackers, the wide-spread use of electronic health records and many others. The sheer volume of the data is not, however, the only challenge to be faced when using medical data for research. Other crucial challenges include data heterogeneity, data quality, data privacy and so on. In this article, we review solutions addressing these challenges by discussing the current state of the art in the areas of data integration, data cleaning, data privacy, scalable data access and processing in the context of medical data. The techniques and tools we present will give practitioners — computer scientists and medical researchers alike — a starting point to understand the challenges and solutions and ultimately to analyse medical data and gain better and quicker insights