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Study of Computing Consolidation Techniques in Computational Protein Loop Structure Modeling

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Executive Summary

In this paper, the authors advocate the approach of "Computing Consolidation" to achieve efficient usage of computer resources in protein structural modeling applications. The fundamental idea of computing consolidation is to increase computational density to a processor in order to increase CPU and other resources utilization rate. They use their computational protein loop structure modeling application with clear memory-intensive and computation-intensive energy function evaluation components as an example to investigate the effectiveness of computing consolidation. They study various implementations of computing consolidation, including process consolidation, fine-grain and coarse-grain thread consolidations on a variety of hardware architectures.

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