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If the job is running from the command line, how about breaking the LVS run into two steps and using a script to run both parts of the LVS and insert the .INCLUDE statement into the layout netlist automatically. Maybe a few lines of the script would look similar to this:
% calibre -spice layout.spi rules > log.extract
% echo ".INCLUDE myotherfile.spi" >> layout.spi
% calibre -layout layout.spi -lvs -hier rules > log.comparison
Thanks. When I do this way will I still be able to probe into the errors in my layout through the RVE?
Yes, should work fine.