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Commercial FPGA companies now provide tools that allow users to implement designs comprising soft-core processors and modules of dedicated logic. If a designer chooses to partition a system into multiple processors and hardware modules, tools and techniques for design analysis are necessary to understand system performance. This work introduces WOoDSTOCK, a tool that profiles system performance by adding monitors to the circuit running in real time on the chip. The user is able to generate a system specific profiler tailored to monitor the communication links between the different computing elements. This provides a macroscopic picture of system performance, which highlights the computing elements that cause bottlenecks in the design.