Paper Citing NAMD - Abstract
Cao, X.L.; Mo, Z.Y.
A new scalable parallel method for molecular dynamics based on cell-block data structure
PARALLEL AND DISTRIBUTED PROCESSING AND APPLICATIONS, PROCEEDINGS, 3358:757-764, 2004
A scalable parallel algorithm especially for large-scale three dimensional simulations with seriously non-uniform particles distributions is presented. In particular, based on cell-block data structures. this algorithm uses Hilbert space filling curve to convert three-dimensional domain decomposition for load distribution across processors into one-dimensional load balancing problems for which measurement-based multilevel averaging weights(MANV) method can be applied successfully. Against inverse space-filling partitioning(ISP), MAW redistributes blocks by monitoring change of total load in each processor. Numerical experimental results have shown that MAW is superior to ISP in rendering balanced load for large-scale multi-medium MD) simulation in high temperature and high pressure physics. Excellent scalability was demonstrated, with a speedup larger than 200 with 240 processors of one MPP. The largest run with 1.1 x 10(9) particles on 500 processors took 80 seconds per time step.
