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there's an option in calibre that you can select to point out what sort of comparison are you going to do...for instance you can go to INPUTS select "Netlist vs netlist" for SVS and "Layout vs Netlist" for LVS.
layout vs layout is generally done when you get a gsdii from customer and you streamin that gdsii to your flow for use..... the first step is to do the lvl, in lvl we need to specify both the gdsii files (different name for both gdsii) but the cell name should be same for both.
eg. - calibre.pl -lvl -gds cc1.gds -cell cc -gds cc2.gds -cell cc
this command is based on the flow set at your workplace, but this will give you some idea.
lvl is done just to conform that while streamin no layer is dropped out.
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