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Parallelizing a molecular dynamics algorithm on a multiprocessor workstation using OpenMP
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DOI：10.1021/ci050126l.png)
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The atomistic Molecular dynamics program YASP has been parallelized for shared-memory computer architectures. Parallelization was restricted to the most CPU-time-consuming parts: neighbor-list construction, calculation of nonbonded, angle and dihedral forces, and constraints. Most of the sequential FORTRAN code was kept; parallel constructs were inserted as compiler directives using the OpenMP standard. Only in the case of the neighbor list did the data structure have to be changed. The parallel code achieves a useful speedup over the sequential version for systems of several thousand atoms and above. On an IBM Regatta p690+, the throughput increases with the number of processors LIP to a maximum of 12-16 processors depending on the characteristics of the simulated systems. On dual-processor Xeon systems, the speedup is about 1.7.
Keyword:
PROTEIN CALCULATIONS
SIMULATION
MD
PROCESSORS
EFFICIENCY
PACKAGE
FORCES
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