@User: This is often a problem with tools that put contact cuts into their own cell, which is incompatible with the way magic represents contacts. Try running the command "gds flatten true" before "gds read ...". That automatically flattens trivially small cells like contacts while leaving everything else as-is. Ultimately, if you have validated the layout on commercial tools, what you want to do is use "gds readonly true" before "gds read", which tells magic to record the extents of data of each cell in the GDS file, so it can use the cell without altering the GDS mask data.

Oh, I see. Thanks for the reply. The M1M2_VIA is still missing the in the magic. I ran through the following command:

gds readonly true
gds flatten true
gds read xxx.gds
load xxx(top cell name)

Not sure whether this is correct or not. But the M1M2_VIA2 is still missing. However, I was able to save a copy of the design from DEF to .mag and performed extraction on the mag file instead. If this sounds good to you, then I will have no problem at this issue now. Another thing I am concerned about is if magic is going to alter the GDS provided by innovus, then how would efabless perform the drc and lvs of our design? Do we need to indicate explicitly that our design is generated by innovus and needs extra care? Thanks for always being supportive!

@Can Wang: The "readonly true" option is what prevents magic from altering the contents of GDS. efabless uses this method when compositing the user project and the caravel harness.