NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Parallel Programming in C with MPI and OpenMP
Parallel Programming in C with MPI and OpenMP
Pore Networks Simulation with Parallel Greedy Algorithms
DS-RT '12 Proceedings of the 2012 IEEE/ACM 16th International Symposium on Distributed Simulation and Real Time Applications
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A parallel simulator, based on the Dual Site-Bond Model of complex media, is developed to study Hg intrusion and extrusion processes in the myriad of voids contained in a porous network. In order to reduce the requirements in RAM and computing resources, the porous network is partitioned into several sub-networks distributed in different cluster processors. The simulator uses shared memory to process (with OpenMP) each sub-network and applies a message passing protocol (with MPI) to allow communication among different processors. We show experimental results that reflect a good performance of our proposal when using different sizes of porous networks in a cluster with 32 nodes, each one having 4 processors.