Diagnosing applications that use hardware acceleration can include emulating, using a processor, a kernel designated for hardware acceleration by executing a device program binary implementing a register transfer level simulator for the kernel. The device program binary is executed in coordination with a host binary and a static circuitry binary. During the emulation, error conditions may be detected using diagnostic program code of the static circuitry binary. The error conditions may relate to memory access violations or kernel deadlocks. A notification of error conditions may be output.