I am struggling to load most of the Drug Ontology OWL files and most of the ChEBI OWL files into GraphDB free v8.3 repository with Optimized OWL Horst reasoning on.
@MarkMiller you can take a look at the Preload tool, which is part of GraphDB 8.4.0 release. It's specially designed to handle large amount of data with constant speed. Note that it works without inference, so you'll need to load your data and then change the ruleset and reinfer the statements.
http://graphdb.ontotext.com/documentation/free/loading-data-using-preload.html