Parallel Molecular Dynamics Using OpenMP on a Shared Memory Machine

Article dans revue scientifique avec comité de lecture.The parallelization of a sequentiel molecular dynamics (MD) program using OpenMP directives for a Fortran compiler is described. The strength of this approach lies in the possibility to proceed incrementally, with no to only few alterations of the original, scalar code. If do-loop splitting with OpenMP is certainly less effecient than domain decomposition (DD) approaches, its fast implementation, requiring little knowledge of the source code, also involves significantly less programming effort. Efficiency of the parallel executable is probed on a distributed-shared memory Silicon Graphics Origin 2000 for MD applications of various complexities. Linear wallclock speed-up ratios using four processors, and ranging between 6.0 and 7.0 with eight, undeline the cost-effectiveness of OpenMP directives for fine-grained MD simulations on limited computational resources