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How to make the file appear?
Another thing: after start ndo2db in console and restart nagios, in nagios web-interface status of objects and services are not update unless kill ndo and restart nagios again. This is due to lack of file?
If you are killing the ndo2db service, that is why none of your host and services are being added to the MYSQL database. The ndo2db service is what puts them in there.
Start up the ndo2db and nagios services, let them run for a long time to see it they get updated. Since you have a lot to add to the database, it might take a while to do so.
While it it running, run the following to see if the ndo2db.lock and ndo.sock files are created.