Reconfigurable computing obtains its performance advantage over fixed processors by creating hardware configurations specialized for a particular application. In some cases this advantage can be pushed even further, by creating hardware specialized to a particular instance of an application. For many problems where this approach is applicable, such as automatic target recognition, template matching, and encryption, the problem parameters can change often even within a single program execution, requiring periodic, and potentially expensive, hardware reconfigurations. To support these applications, we propose a method for on-chip configuration generation, or embedded compilation, for use with CMU's PipeRench reconfigurable processor. We describe PipeRench's performance in detail for one problem, template matching, relative to the newest general-purpose processors, and show how embedded compilation can be used to support multiple problem instances for a second problem, IDEA encryption.