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

A Taxonomy of Workflow Management Systems for Grid Computing

With the advent of Grid and application technologies, scientists and engineers are building more and more complex applications to manage and process large data sets, and execute scientific experiments on distributed resources. Such application scenarios require means for composing and executing complex workflows. Therefore, many efforts have been made towards the development of workflow management systems for Grid computing. In this paper, we propose a taxonomy that characterizes and classifies various approaches for building and executing workflows on Grids. We also survey several representative Grid workflow systems developed by various projects world-wide to demonstrate the comprehensiveness of the taxonomy. The taxonomy not only highlights the design and engineering similarities and differences of state-of-the-art in Grid workflow systems, but also identifies the areas that need further research.Comment: 29 pages, 15 figure

A Logical Model and Data Placement Strategies for MEMS Storage Devices

MEMS storage devices are new non-volatile secondary storages that have outstanding advantages over magnetic disks. MEMS storage devices, however, are much different from magnetic disks in the structure and access characteristics. They have thousands of heads called probe tips and provide the following two major access facilities: (1) flexibility: freely selecting a set of probe tips for accessing data, (2) parallelism: simultaneously reading and writing data with the set of probe tips selected. Due to these characteristics, it is nontrivial to find data placements that fully utilize the capability of MEMS storage devices. In this paper, we propose a simple logical model called the Region-Sector (RS) model that abstracts major characteristics affecting data retrieval performance, such as flexibility and parallelism, from the physical MEMS storage model. We also suggest heuristic data placement strategies based on the RS model and derive new data placements for relational data and two-dimensional spatial data by using those strategies. Experimental results show that the proposed data placements improve the data retrieval performance by up to 4.0 times for relational data and by up to 4.8 times for two-dimensional spatial data of approximately 320 Mbytes compared with those of existing data placements. Further, these improvements are expected to be more marked as the database size grows.Comment: 37 page