I started the cloudera manager building the nodes but ran out of space while installing apperantly.
I repartitioned and rebuild the compute nodes.
Now after I do the host scan It thinks they all have agents installed but they dont and I dont see how to convince it otherwise.
Do I just delete the scm database and recreate it?
You could just start everything over, but that is not necessary for what you want to do.
At this point it sounds as if you do not have any agent running on the hosts you rebuilt but you still see them in Cloudera Manager's Hosts tab.
You can delete these hosts from the CM database with the following steps:
Once the hosts are deleted from CM, you can use the Add New Hosts to Cluster button to start the wizard.