The Ames Lab Classical Molecular Dynamics code has a 3D simulation space with periodic boundary conditions filled with atoms that interact using classical potentials. A 2D decomposition is used to divide the 3D simulation space among the processors, with neighboring columns being assigned to neighboring nodes on the network to localize the communications. The picture shows the CMD code mapped to the 2D mesh of an old Intel Paragon. On this architecture, communications to calculate the interatomic forces involve global shifts of the atomic positions in the vertical and horizontal directions.

Both the memory and CPU load are decomposed among the processors, making this approach very scalable. If the 2D virtual topology can be mapped to the actual topology of the underlying network, communications will be localized (no contention for communication channels) and the code will scale very efficiently to large numbers of processors.