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In a typical design flow, an FPGA application developer will simulate the design at multiple stages throughout the design process.
Initially the RTL description in VHDL or Verilog is simulated by creating test benches to simulate the system and observe results.
Then, after the synthesis engine has mapped the design to a netlist, the netlist is translated to a gate level description where simulation is repeated to confirm the synthesis proceeded without errors.
Finally the design is laid out in the FPGA at which point propagation delays can be added and the simulation run again with these values back-annotated onto the netlist.

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