Web-based Grid PSE for MD Simulations using Grid PSE Builder

In large-scale scientific simulations, we sometimes have access to supercomputers and largescale cluster systems of appropriate computer centers at remote sites as a way of obtaining large scale computer resources. In this case, some difficulties in using such resources due to differences in rules and job execution at each computer center have been found. Differences among remote sites to be accessed might contribute a delay in research and development, since it takes time for the application-side researcher to get to know a new computer environment well. In order to provide a common environment to users, we have constructed an MD Portal or a web-based PSE for parallel MD simulations using Grid PSE Builder, a portal construction tool for PSE developers on the Grid. Users can obtain common “look and feel” interfaces to carry out their MD simulations through a Grid PSE, regardless of differences in computer resources. Multi-site computer environments are obscured from user's eyes. The MD Portal has two components; one is an MD kernel component using the parallel MD Web-based Grid PSE for MD Simulations using Grid PSE Builder Naotaka Yamamoto, Futoshi Shimizu, Mitsuo Yokokawa, Satoshi Sekiguchi, Hideo Kaburaki, Motoyoshi Kurokawa, and Ryutaro Himeno Naotaka Yamamoto, Futoshi Shimizu, Mitsuo Yokokawa, Satoshi Sekiguchi, Hideo Kaburaki, Motoyoshi Kurokawa, Ryutaro Himeno Web-based Grid PSE for MD Simulations using Grid PSE Builder 60 Stencil library, and the other is an image generator component for drawing snapshots of the results of MD simulations. Users can submit their jobs with their own parameters, check job status, and manage result files from their jobs through a web browser with secure connections. The image generator provides an animation of the results. We have confirmed the effectiveness of the Grid PSE by applying it to an MD simulation for calculating the intrinsic transformation of the vacancy dislocation loop in copper crystal. Keyword: Grid, Grid PSE, Grid Portal, Molecular Dynamics