The problem is less of scheduling and more of communication. Typically all nodes will run (facilitated by a program like mpirun or mpiexec) the same executable which will be launched simultaneously in each OS. This is done inside a job scheduler and the resulting host list results in a defined communication pattern.

By the way, even systems completely across the room may be "close" to each other, depending on the topology of the system. You can imagine this being important for solving a physical system which is periodic in certain dimensions, so there should be little interconnect distance between physically-distant nodes.