Resource run-time managers have been shown par- ticularly effective for coordinating the usage of the hardware resources by multiple applications, eliminating the necessity of a full-blown operating system. For this reason, we expect that this technology will be increasingly adopted in emerging multi- application reconfigurable systems. This paper introduces a fully automated design flow that exploits multi-objective design space exploration to enable run- time resource management for the Molen reconfigurable archi- tecture. The entry point of the design flow is the application source code; our flow is able to heuristically determine a set of candidate hardware/software configurations of the application (i.e., operating points) that trade o...