First: the correct error message is “map has no nodes” (verbatim error messages make searching way easier, I had to grep the game binary for “node” to figure out why Google wasn’t returning any hits).
The interwebs have various possible explanations how this could happen and no clean and simple answer, but the underlying reason is that the BSP volume has not been created during compile (“no nodes”), i.e. something in the map construction is preventing the compiler from interpreting the structural brushes correctly and the map has no “inside”. Look for brush entities that shouldn’t be there — the most likely way this could happen is that you have accidentally selected the whole map and turned it into an entity, making the worldspawn empty. Press L to see the entity list (also found in the View menu) and take a look at the bottom of the list to see if the worldspawn contains any brushes. To fix this, select the bad brushes and do Entity → Ungroup.
If this doesn’t help, upload the .MAP file and I’ll take a look.