Scheduling malleable tasks with interdependent processing rates: Comments and observations
Discrete Applied Mathematics
An FPGA design to achieve fast and accurate results for molecular dynamics simulations
ISPA'07 Proceedings of the 5th international conference on Parallel and Distributed Processing and Applications
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This paper aims to describe the implementation of TAKAKAW, an efficient parallel application for the simulation of molecular dynamics designed to handle large proteins in biology. The implementation is based on the multi-threading parallel programming environment, called ATHAPASCAN 1 which allows to implement and evaluate easily several load-balancing strategies. Some experiments run on one of the largest molecule ever simulated (a hydrated β-galactosidase with 413039 atoms) show the interest of such a parallel programming environment.Keywords. Load balancing - Threads - Parallel Molecular Dynamics