System on a chip FPGA spatial debugging using single snapshot

A method for performing on-chip spatial debugging of a user circuit programmed into a user-programmable integrated circuit includes halting an internal clock driving synchronous logic elements in the integrated circuit and reading the states of all synchronous logic elements programmed into the integrated circuit while the internal clock is halted. An interrupt to an embedded processor in the integrated circuit running a user application can also be generated. The output of at least one synchronous logic element can be forced to a desired state while the internal clock is halted. The clock can then be restarted or stepped.