The technology disclosed provides a system that comprises a processor with computing units on an integrated circuit substrate. The processor is configured to map a program across multiple hardware stages with each hardware stage executing a corresponding operation of the program at a different stage latency dependent on an operation type and an operand format. The system further comprises a runtime logic that configures the compute units with configuration data. The configuration data causes first and second producer hardware stages in a given compute unit to execute first and second data processing operations and produce first and second outputs at first and second stage latencies, and synchronizes consumption of the first and second outputs by a consumer hardware stage in the given compute unit for execution of a third data processing operation by introducing a register storage delay that compensates for a difference between the first and second stage latencies.