A method, apparatus, and computer program product for scheduling stream-based applications in a distributed computer system with configurable networks are provided. The method includes choosing, at a highest temporal level, jobs that will run, an optimal template alternative for the jobs that will run, network topology, and candidate processing nodes for processing elements of the optimal template alternative for each running job to maximize importance of work performed by the system. The method further includes making, at a medium temporal level, fractional allocations and re-allocations of the candidate processing elements to the processing nodes in the system to react to changing importance of the work. The method also includes revising, at a lowest temporal level, the fractional allocations and re-allocations on a continual basis to react to burstiness of the work, and to differences between projected and real progress of the work.