The HAPI JPA Server (the CDR above is a version of this) uses RDBMS storage but it stores all the resources in a column in one table. This is for the reasons Rik just listed.
If you get HAPI running locally with a hibernate compatible database (postgresql, mysql, sql server, etc) it will build the database for you.
The CCRI (which is also the CDR-Sql above) will also build a database (again it uses hibernate but has only been tested on postgresql). It is not a complete set of FHIR resources but these do get broken down into a traditional RDBMS structure.
Both need some familiarity with java to configure.