A Grid-Based Cyber Infrastructure for High Performance Chemical Dynamics Simulations

• Main Authors: Khadka Prashant, Yu Zhuang, Upakarasamy Lourderaj, William L. Hase
• Format: Article
• Language: English
• Published: International Institute of Informatics and Cybernetics 2008-10-01
• Series: Journal of Systemics, Cybernetics and Informatics
• Online Access: http://www.iiisci.org/Journal/CV$/sci/pdfs/I462RV.pdf

Chemical dynamics simulation is an effective means to study atomic level motions of molecules, collections of molecules, liquids, surfaces, interfaces of materials, and chemical reactions. To make chemical dynamics simulations globally accessible to a broad range of users, recently a cyber infrastructure was developed that provides an online portal to VENUS, a popular chemical dynamics simulation program package, to allow people to submit simulation jobs that will be executed on the web server machine. In this paper, we report new developments of the cyber infrastructure for the improvement of its quality of service by dispatching the submitted simulations jobs from the web server machine onto a cluster of workstations for execution, and by adding an animation tool, which is optimized for animating the simulation results. The separation of the server machine from the simulation-running machine improves the service quality by increasing the capacity to serve more requests simultaneously with even reduced web response time, and allows the execution of large scale, time-consuming simulation jobs on the powerful workstation cluster. With the addition of an animation tool, the cyber infrastructure automatically converts, upon the selection of the user, some simulation results into an animation file that can be viewed on usual web browsers without requiring installation of any special software on the user computer. Since animation is essential for understanding the results of chemical dynamics simulations, this animation capacity provides a better way for understanding simulation details of the chemical dynamics. By combining computing resources at locations under different administrative controls, this cyber infrastructure constitutes a grid environment providing physically and administratively distributed functionalities through a single easy-to-use online portal