After renaming a file in place, the dbpath directory must also be flushed before a rename is durable. After renaming the storage.bson file, the dbpath's parent is accidentally being flushed. This provides the durability guarantee, but the mongod process may not have permissions to do so. This results in an exception crashing mongod.

Problematic verbose log line when starting on the default dbpath of /data/db/:

2017-10-05T14:18:52.806-0400 D STORAGE  [initandlisten] flushing directory /data

The fixed version:

2017-10-05T14:21:39.449-0400 D STORAGE  [initandlisten] flushing directory /data/db