SC is the International Conference for
 High Performnance Computing, Networking, Storage and Analysis

SCHEDULE: NOV 13-19, 2010

Task-Parallel MPI Implementation of Autodock4 for Docking of Very Large Databases of Compounds using High Performance Super-Computers

SESSION: Research Poster Reception


TIME: 5:15PM - 7:00PM

AUTHOR(S):Barbara Collignon, Roland Schulz, Jeremy Smith, Jerome Baudry

ROOM:Main Lobby

An MPI-based implementation (Autodock4.lga.MPI) of the grid-based docking program Autodock4 has been developed to allow simultaneous and independent docking of multiple compounds on up to thousands of CPUs using the Lamarkian Genetic Algorithm (LGA). The MPI version reads a single binary file containing precalculated grids that represent the protein-ligand interactions, and needs only two input parameter files for the entire docking run. In comparison, the serial version of Autodock4 reads ASCII grid files and requires one parameter file per compound. Autodock4.lga.MPI scales up to 8,192 CPUs with a maximal overhead of 16.3%. The optimal docking strategy, that minimizes docking CPU time, comprises the docking of ligands pre-ordered from the most to the least flexible and the assignment of the number of energy evaluations as a function of the number of rotatable bounds. In 24 hours, on 8,192 HPC CPUs, the present MPI version would allow docking to a rigid protein of about 300K flexible compounds or 11 million rigid compounds.

Chair/Author Details:

Barbara Collignon - University of Tennessee, Knoxville

Roland Schulz - University of Tennessee, Knoxville

Jeremy Smith - University of Tennessee, Knoxville

Jerome Baudry - University of Tennessee, Knoxville

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