PETASCALE MOLECULAR DYNAMICS DATA PROCESSING

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Biomedically-relevant cell-scale processes take place in molecular assemblies made of millions to hundreds of millions of atoms. Atomistic molecular dynamics simulation of these structures provides insight into their functional mechanisms; such simulations are extremely demanding and require petascale computational resources. The datasets that result are so large that existing workstations are too limited  in physical memory, processing and visualization power, and mass storage  to efficiently handle them. Common visualization calculations, such as three-dimensional maps of electrostatic potential fields across a long trajectory, can take minutes using a standard desktop workstation. As a result, a researcher's interactive analysis of a large simulation result is interrupted and slowed so much as to be virtually impossible; the Petascale Molecular Dynamics Data Processing System (MDDPS) is designed to overcome the shortcomings of desktop computer workstations and provides the necessary hardware features to enable practical interactive analysis and visualization of challenging petascale datasets. The Petascale MDDPS is a cluster of tightly coupled computers that operate as a cohesive unit to provide high-performance data analysis capabilities required by petascale MD simulations. The system is composed of synergistic storage, analysis, and visualization nodes connected internally and to external resources by separate high-speed networks. While both of the Resource's software packages, NAMD and VMD, are well-tuned to current computer hardware, harnessing the next-generation capabilities of the Petascale MDDPS hardware requires additional software development.