reasoner never finishes query

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I am having some trouble with ELK queries on a large dataset. I have an OWL 
ontology in a 778 MB RDF/XML file. Using ELK I can precompute the class 
hierarchy for this ontology within several minutes. The process uses about 8 GB 
of RAM out of the 12 GB I allocated it. When I query for subclasses of an 
anonymous class expression, it returns the answer in less than a second. When I 
query a second class expression, the memory usage rapidly increases to 12 GB 
and all (4) CPUs are maxed out. In the log I see that ELK messages are printed 
up to this point:

INFO  org.semanticweb.elk.reasoner.stages.AbstractReasonerStage  - Incremental 
Deletion using 4 workers

It never proceeds beyond there, after waiting more than an hour. The particular 
class expression doesn't matter. If I have two ObjectSomeValuesFrom 
restrictions, A and B, I can query A in less than a second and then have B go 
out of control. If I query B first, then querying A will go out of control.

It is somewhat confusing because within a different application I have 
previously used ELK for datasets of this size. However I can reproduce the 
problem with this small Scala application:

https://github.com/balhoff/test-elk/blob/dd6d9328adc119b993b455ea732399fd581a616
9/src/main/scala/org/nescent/Main.scala

I encountered the issue with ELK 0.4.0, 0.4.1, and a nightly build from 
2014-09-22.

My ontology can be downloaded from here: 
https://dl.dropboxusercontent.com/u/6704325/elk-query/tbox.owl.gz

Original issue reported on code.google.com by [email protected] on 23 Sep 2014 at 4:20