3D Visualization of Molecular Simulations in High-performance Parallel Computing Environments* KARSTEN MEIER a,† , CHRISTOPHER HOLZKNECHT a , STEPHAN KABELAC a , STEPHAN OLBRICH b and KARSTEN CHMIELEWSKI b a Institute for Thermodynamics, University of the Federal Armed Forces Hamburg, Holstenhofweg 85, D-22043 Hamburg, Germany; b Regional Scientific Computing Centre for Lower Saxony, University of Hannover, Schloßwender Str. 5, D-30159 Hannover, Germany (Received July 2003; In final form February 2004) This paper presents a novel tool for interactive 3D visualization and computational steering of molecular simulations and other computer simulation techniques such as computational fluid dynamics in parallel comput- ing environments. The visualization system consists of three major components—data source, streaming server and viewer—which are distributed in intra/internet net- works. A parallelized data extraction and visualization library, which generates 3D scenes, is integrated in the simulation software. The 3D scenes can be stored locally or sent to the streaming server parallel to the simulation, where they are stored on a fast RAID hard disk system. The streaming server transfers the 3D scenes to viewer clients on demand for display. A multi-platform 3D viewer software is provided as a plug-in embeddable into different WWW browsers. Many models of broad interest in molecular simulations can be visualized, from simple spherical particles to moderately complex molecules, and several volume visualization methods are implemented efficiently. Examples from thermophysical property research applications demonstrate the utility of the visualization system. One example shows that the transport coefficients of the Lennard – Jones fluid at subcritical temperatures in the gas region are influenced by the formation of small clusters of particles. Keywords: 3D visualization; Cluster formation; Lennard–Jones potential; Molecular simulation; Parallel computing INTRODUCTION 3D visualization of molecular simulations can help to interpret simulation results and can contribute significantly to the understanding of mechanisms on the molecular scale, which are responsible for the macroscopic behavior of fluids. For example, when 3D scene sequences from simulations are visualized as smooth animations, the motion of individual particles or groups of particles can be followed easily, giving the simulator direct visual insights into the dynamics on the molecular scale. Molecular simulations employing a few hundred molecules of moderate complexity already require large computational resources. Therefore, they are usually carried out on high-performance parallel computers. The addition and integration of a visualization into the simulation software turns out to be a challenging task, especially if it is intended to build an efficient, balanced and scalable process chain and to add only a small additional computational cost on the simulation. The aim of this paper is to provide a novel network-distributed visualization system for inter- active 3D visualization of molecular simulations in high-performance parallel computing environments. Major differences of the system presented in this paper to other visualization systems are as follows: firstly, the software and the format of the data are optimized for speed and cover a wide range of 3D visualization primitives. Second, a streaming system enables us to explore 3D scenes while the simulation is in progress without access to local hard disks. Moreover, the system can be used in environments with a combination of shared and distributed memory architectures. Interactive navigation of ISSN 0892-7022 print/ISSN 1029-0435 online q 2004 Taylor & Francis Ltd DOI: 10.1080/08927020410001680778 *Paper presented at FOMMS 2003—Foundations of Molecular Modeling and Simulation, July 6–11, 2003, Keystone, Colorado, USA. † Corresponding author. Tel.: þ49-0-40-6541-2161. Fax: þ 49-0-40-6541-2005. E-mail: karsten.meier@unibw-hamburg.de Molecular Simulation, Vol. 30 (7), 15 June 2004, pp. 469–477