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High Performance Parallelism Pearls Volume Two by James Reinders, Jim Jeffers

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Chapter 5

Accelerated Structural Bioinformatics for Drug Discovery

Wei P. Feinstein; Michal Brylinski    Louisiana State University, USA

Abstract

This chapter documents the parallelization of, eFindSite, a ligand binding site prediction software used in drug discovery and design. eFindSite is a complex hybrid C++/Fortran77 code, which includes significant legacy Fortran software that was not thread-safe, to utilize parallelism and obtain a 17.6× speedup. Solutions to challenges in moving this code to parallelism serve as lessons with wide applicability and are examined in detail. Porting extensive use of thread-unsafe common blocks in the Fortran77 code using OpenMP to make thread-private copies is discussed. With minimal modifications, it ...

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