title: DCMS: A data analytics and management system for molecular simulation.
abstract: Molecular Simulation (MS) is a powerful tool for studying physical/chemical features of large systems and has seen applications in many scientific and engineering domains. During the simulation process, the experiments generate a very large number of atoms and intend to observe their spatial and temporal relationships for scientific analysis. The sheer data volumes and their intensive interactions impose significant challenges for data accessing, managing, and analysis. To date, existing MS software systems fall short on storage and handling of MS data, mainly because of the missing of a platform to support applications that involve intensive data access and analytical process. In this paper, we present the database-centric molecular simulation (DCMS) system our team developed in the past few years. The main idea behind DCMS is to store MS data in a relational database management system (DBMS) to take advantage of the declarative query interface (i.e., SQL), data access methods, query processing, and optimization mechanisms of modern DBMSs. A unique challenge is to handle the analytical queries that are often compute-intensive. For that, we developed novel indexing and query processing strategies (including algorithms running on modern co-processors) as integrated components of the DBMS. As a result, researchers can upload and analyze their data using efficient functions implemented inside the DBMS. Index structures are generated to store analysis results that may be interesting to other users, so that the results are readily available without duplicating the analysis. We have developed a prototype of DCMS based on the PostgreSQL system and experiments using real MS data and workload show that DCMS significantly outperforms existing MS software systems. We also used it as a platform to test other data management issues such as security and compression.
authors.affiliation: Department of Computer Science and Engineering, University of South Florida, 4202 E. Fowler Ave., ENB118, Tampa, 33620 Florida USA.
authors.forename: Anand
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Department of Computer Science and Engineering, University of South Florida, 4202 E. Fowler Ave., ENB118, Tampa, 33620 Florida USA.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Grupcev
authors.affiliation: Department of Computer Science and Engineering, University of South Florida, 4202 E. Fowler Ave., ENB118, Tampa, 33620 Florida USA.
authors.forename: Meryem
authors.initials: M
authors.lastname: Berrada
authors.affiliation: Department of Physics, University of South Florida, 4202 E. Fowler Ave., PHY114, Tampa, 33620 Florida USA.
authors.forename: Joseph C
authors.initials: JC
authors.lastname: Fogarty
authors.affiliation: Department of Computer Science and Engineering, University of South Florida, 4202 E. Fowler Ave., ENB118, Tampa, 33620 Florida USA.
authors.forename: Yi-Cheng
authors.initials: YC
authors.lastname: Tu
authors.affiliation: Department of Electrical Engineering and Computer Science, Florida Atlantic University, 777 Glades Road, EE308, Boca Raton, 33431 Florida USA.
authors.forename: Xingquan
authors.initials: X
authors.lastname: Zhu
authors.affiliation: Department of Physics, University of South Florida, 4202 E. Fowler Ave., PHY114, Tampa, 33620 Florida USA.
authors.forename: Sagar A
authors.initials: SA
authors.lastname: Pandit
authors.affiliation: Department of Computer Science, Indiana University - Purdue University Indianapolis, 723 W. Michigan St, SL280E, Indianapolis, 46202 Indiana USA.
authors.forename: Yuni
authors.initials: Y
authors.lastname: Xia
keywords: Data compression; Molecular dynamics; Molecular simulation; Scientific database; Spatiotemporal database