Benchmarking SciDB Data Import on HPC Systems

SciDB is a scalable, computational database management system that uses an array model for data storage. The array data model of SciDB makes it ideally suited for storing and managing large amounts of imaging data. SciDB is designed to support advanced analytics in database, thus reducing the need for extracting data for analysis. It is designed to be massively parallel and can run on commodity hardware in a high performance computing (HPC) environment. In this paper, we present the performance of SciDB using simulated image data. The Dynamic Distributed Dimensional Data Model (D4M) software is used to implement the benchmark on a cluster running the MIT SuperCloud software stack. A peak performance of 2.2M database inserts per second was achieved on a single node of this system. We also show that SciDB and the D4M toolbox provide more efficient ways to access random sub-volumes of massive datasets compared to the traditional approaches of reading volumetric data from individual files. This work describes the D4M and SciDB tools we developed and presents the initial performance results. This performance was achieved by using parallel inserts, a in-database merging of arrays as well as supercomputing techniques, such as distributed arrays and single-program-multiple-data programming.Comment: 5 pages, 4 figures, IEEE High Performance Extreme Computing (HPEC) 2016, best paper finalis

Enabling On-Demand Database Computing with MIT SuperCloud Database Management System

The MIT SuperCloud database management system allows for rapid creation and flexible execution of a variety of the latest scientific databases, including Apache Accumulo and SciDB. It is designed to permit these databases to run on a High Performance Computing Cluster (HPCC) platform as seamlessly as any other HPCC job. It ensures the seamless migration of the databases to the resources assigned by the HPCC scheduler and centralized storage of the database files when not running. It also permits snapshotting of databases to allow researchers to experiment and push the limits of the technology without concerns for data or productivity loss if the database becomes unstable.Comment: 6 pages; accepted to IEEE High Performance Extreme Computing (HPEC) conference 2015. arXiv admin note: text overlap with arXiv:1406.492

An efficient parallel method for mining frequent closed sequential patterns

Mining frequent closed sequential pattern (FCSPs) has attracted a great deal of research attention, because it is an important task in sequences mining. In recently, many studies have focused on mining frequent closed sequential patterns because, such patterns have proved to be more efficient and compact than frequent sequential patterns. Information can be fully extracted from frequent closed sequential patterns. In this paper, we propose an efficient parallel approach called parallel dynamic bit vector frequent closed sequential patterns (pDBV-FCSP) using multi-core processor architecture for mining FCSPs from large databases. The pDBV-FCSP divides the search space to reduce the required storage space and performs closure checking of prefix sequences early to reduce execution time for mining frequent closed sequential patterns. This approach overcomes the problems of parallel mining such as overhead of communication, synchronization, and data replication. It also solves the load balance issues of the workload between the processors with a dynamic mechanism that re-distributes the work, when some processes are out of work to minimize the idle CPU time.Web of Science5174021739

Supporting Complex Scientific Database Schemas in a Grid Middleware

“This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder." “Copyright IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.” DOI: 10.1109/AINA.2009.129The volume of digital scientific data has increased considerably with advancing technologies of computing devices and scientific instruments. We are exploring the use of emerging Grid technologies for the management and manipulation of very large distributed scientific datasets. Taking as an example a terabyte-size scientific database with complex database schema, this paper focuses on the potential of a well-known Grid middleware - OGSA-DQP - for distributing such datasets. In particular, we investigate and extend the data type support in this system to handle a complex schema of a real scientific database - the Sloan Digital Sky Survey database