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Exploiting Multi-level Parallelism on a Many-core System for the Application of Hyperheuristics to a Molecular Docking Problem

Jose M. Cecilia, Jose-Matias, Cutillas-Lozano, Domingo Gimenez, Baldomero Imbernon
Polytechnic School, Catholic University of San Antonio of Murcia (UCAM), Spain
The Journal of Supercomputing, 2017

@article{imbernon2017exploiting,

   title={Exploiting Multi-level Parallelism on a Many-core System for the Application of Hyperheuristics to a Molecular Docking Problem},

   author={Imbern{‘o}n, Baldomero},

   year={2017}

}

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The solution of Protein-Ligand Docking Problems can be approached through metaheuristics, and satisfactory metaheuristics can be obtained with hyperheuristics searching in the space of metaheuristics implemented inside a parameterized schema. These hyperheuristics apply several metaheuristics, resulting in high computational costs. To reduce execution times, a shared-memory schema of hyperheuristics is used with four levels of parallelism, two for the hyperheuristic and two for the metaheuristics. The parallel schema is executed in a many-core system in "native mode", and the four-level parallelism allows us to take full advantage of the massive parallelism offered by this architecture and obtain satisfactory fitness and an important reduction of the execution time.
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