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Web Based Distributed Computing Environment for Nanotechnology

D. Chen, A. Raghunathan, J. Mashl, S. Chiu, S. Parker, N. Aluru and E. Jakobsson
NCSA at UIUC, US

Keywords:
distributed computing, computational, nanotechnology, nanoscale

Abstract:
One promising path of computational nanoscience is the integration of device design tools and computational chemistry tools to design molecular device components. In order to improve the efficiency of the design process and also let the device designer who is not necessarily a computational scientist use these device design tools easily, we have created a web based distributed computing system to connect client layer, web server layer and parallel computing server layer to link the job submission, computation, result retrieval and visualization together, and run the job automatically. This web based distributed computing enterprise, NanoGromacs, employs the open source molecular dynamics package Gromacs for simulation, and the open source visualization program Pymol for visualization. NanoGromacs provides client machine the ability to communicate with the server interactively with job running, which is especially convenient for those jobs in which parameters must be provided based on intermediate results. The web server layer of NanoGromacs is a machine in our laboratory called Peptide and the parallel computing server layer is the NCSA Xeon cluster Tungsten which is composed of 1280 computer nodes. The NanoGromacs is freely accessible to general computational nanoscience community.

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