Xilinx VC709 Manual page 35

Program VC709 with Si5324 Design
Init memory with the Si5324 Application ELF
– Update the bitstream (download.bit) with the Si5324 Application ELF
– Cycle power on the VC709 to clear out any previous settings in the Si5324
– Select Xilinx Tools → Program FPGA (1)
1
Note: Presentation applies to the VC709