Looking at the report, I'd guess that you have a port order mismatch. What command(s) are you using to extract and run lvs?

(no matching net)                          |Net: VDD                                   
                                           |  sky130_fd_sc_hd__nand2_1/Y = 14          
                                           |  sky130_fd_sc_hd__nand2_1/B = 14          
                                           |  sky130_fd_sc_hd__clkinv_2/Y = 1          
                                           |  sky130_fd_sc_hd__clkinv_2/VGND = 1       
                                           |  sky130_fd_sc_hd__inv_1/Y = 12            
                                           |  sky130_fd_sc_hd__inv_1/VGND = 12         
                                           |  sky130_fd_sc_hd__nor2_1/B = 1            
                                           |  sky130_fd_sc_hd__nor2_1/Y = 1            
                                           |  sky130_fd_sc_hd__inv_2/Y = 1             
                                           |  sky130_fd_sc_hd__inv_2/VGND = 1          
                                           |  sky130_fd_sc_hd__dfstp_1/Q = 10          
                                           |  sky130_fd_sc_hd__dfstp_1/SET_B = 10      
                                           |  sky130_fd_sc_hd__nand3_1/C = 3           
                                           |  sky130_fd_sc_hd__nand3_1/B = 3           
                                           |  sky130_fd_sc_hd__nand2_2/Y = 1           
                                           |  sky130_fd_sc_hd__nand2_2/B = 1           
                                           |  sky130_fd_sc_hd__dfstp_2/Q = 1           
                                           |  sky130_fd_sc_hd__dfstp_2/SET_B = 1

From

NON_CLK_GEN.spice

, I bet the port orders defined in

.INCLUDE '/home/elonjia/OpenROAD-flow-scripts/flow/platforms/sky130hd/cdl/sky130_fd_sc_hd.spice'

don't match the instance calls

X_2_ net5 VDD VSS VSS net1 u_DCDC_NOV_CLKGEN.clk_in9 VDD sky130_fd_sc_hd__nand2_1
X_3_ net4 VDD VSS VSS net5 VDD sky130_fd_sc_hd__clkinv_2
...

@Mitch Bailey, Hi Mitch, I just use this command and script to extract the GDS and do lvs for it. For the original cdl file, it is parsed by a script, then compared with the extract lvsmag.spice using a flattened gds file.

Is

netgen_lvs

a target in a private makefile? Instead of using the cdl models for the standard cells (some won't pass lvs with netgen), you could try to use the spice models.

OK, let me try it, thank you, Mitch!