What about the Cheyenne Mountain Complex where NORAD is housed, or the Raven Rock Complex? They were built to withstand nuclear attacks, and have big ass vault doors that close to seal off the facilities completely in the event of nuclear war or other emergency conditions. They are also stocked with boatloads of supplies, equipment, etc for these contingencies. No way the military didn’t go to DEFCON 1 and seal the place up the moment portals started opening up, or even before that happened once the government knew things were starting to get out of hand.
If there was any kind of command and control or organization that was going to happen after the Cataclysm, these are some of the types of secure places it might be organized out of or based around, and there are LOTS of them; the US was rather concerned about decapitation strikes during the Cold War. There is almost no way all of them got knocked out or overrun. I doubt even a zombie hulk could bash through an 8 foot thick hardened steel vault door. And it would have been completely retarded to put secret laboratories with portals or other hazardous things in them, because you would not want to risk your continuity of government facilities being potentially compromised. Probably why they built them underneath everything else instead.