I think it is this one from stardog.log (below). Apparently it is a query timeout? I don't think the new version is slower than the previous one (normally it is just the opposite and in a greatly way, actually) and I checked and my database has 5m query timeout (300000, as said in the logs) but the application doesn't take 5m to produce an answer, it is less than a minute.
ERROR 2016-06-29 17:17:30,003 [StardogServer.WorkerGroup-4] com.complexible.stardog.protocols.http.server.HttpMessageEncoder:write(161): There was an error while encoding the response
com.complexible.common.protocols.EncodingException: com.complexible.stardog.plan.eval.operator.OperatorException: Query execution cancelled: Execution time exceeded query timeout 300000
at com.complexible.stardog.protocols.http.server.io.ResponseBodyEncoders$13.encode(ResponseBodyEncoders.java:471) ~[stardog-protocols-http-server-4.1.1.jar:?]
at com.complexible.stardog.protocols.http.server.io.ResponseBodyEncoders$2.encode(ResponseBodyEncoders.java:99) ~[stardog-protocols-http-server-4.1.1.jar:?]
at com.complexible.stardog.protocols.http.annex.QueryPanelEncoder.encode(QueryPanelEncoder.java:112) ~[stardog-webconsole-annex-4.1.1.jar:?]
at com.complexible.stardog.protocols.http.server.HttpMessageEncoder.write(HttpMessageEncoder.java:158) [stardog-protocols-http-server-4.1.1.jar:?]
at io.netty.channel.AbstractChannelHandlerContext.invokeWrite(AbstractChannelHandlerContext.java:633) [netty-all-4.0.32.Final.jar:4.0.32.Final]
at io.netty.channel.AbstractChannelHandlerContext.access$1900(AbstractChannelHandlerContext.java:32) [netty-all-4.0.32.Final.jar:4.0.32.Final]
at io.netty.channel.AbstractChannelHandlerContext$AbstractWriteTask.write(AbstractChannelHandlerContext.java:908) [netty-all-4.0.32.Final.jar:4.0.32.Final]
at io.netty.channel.AbstractChannelHandlerContext$AbstractWriteTask.run(AbstractChannelHandlerContext.java:893) [netty-all-4.0.32.Final.jar:4.0.32.Final]
at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:358) [netty-all-4.0.32.Final.jar:4.0.32.Final]
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:357) [netty-all-4.0.32.Final.jar:4.0.32.Final]
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:112) [netty-all-4.0.32.Final.jar:4.0.32.Final]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_66-internal]
Caused by: org.openrdf.query.QueryEvaluationException: com.complexible.stardog.plan.eval.operator.OperatorException: Query execution cancelled: Execution time exceeded query timeout 300000
at com.complexible.common.rdf.query.IteratorAsTupleQueryResult.hasNext(IteratorAsTupleQueryResult.java:81) ~[stardog-utils-rdf-4.1.1.jar:?]
at com.complexible.stardog.protocols.server.ConnectionFinishQueryResult.hasNext(ConnectionFinishQueryResult.java:75) ~[stardog-protocols-spec-server-4.1.1.jar:?]
at com.complexible.stardog.protocols.server.ConnectionFinishQueryResult.next(ConnectionFinishQueryResult.java:91) ~[stardog-protocols-spec-server-4.1.1.jar:?]
at org.openrdf.query.QueryResults.report(QueryResults.java:159) ~[sesame-query-4.0.0.jar:?]
at org.openrdf.query.resultio.QueryResultIO.writeTuple(QueryResultIO.java:449) ~[sesame-queryresultio-api-4.0.0.jar:?]
at com.complexible.stardog.protocols.http.server.io.ResponseBodyEncoders$13.encode(ResponseBodyEncoders.java:468) ~[stardog-protocols-http-server-4.1.1.jar:?]
... 11 more
Caused by: com.complexible.stardog.plan.eval.operator.OperatorException: Query execution cancelled: Execution time exceeded query timeout 300000
at com.complexible.stardog.plan.eval.operator.impl.AbstractOperator.checkCanceled(AbstractOperator.java:139) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.IndexScan.computeNext(IndexScan.java:376) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.IndexScan.computeNext(IndexScan.java:40) ~[stardog-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:143) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:130) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.SimpleEquiJoinKeyIterator.hasNext(SimpleEquiJoinKeyIterator.java:93) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.ResetableEquiJoinIterator.hasNext(ResetableEquiJoinIterator.java:106) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.MergeJoinOp$InnerJoinCrossProductIterator.hasNext(MergeJoinOp.java:539) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.MergeJoinOp._nextCross(MergeJoinOp.java:162) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.MergeJoinOp.computeNext(MergeJoinOp.java:236) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.MergeJoinOp.computeNext(MergeJoinOp.java:34) ~[stardog-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:143) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:130) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.LoopJoin.computeNext(LoopJoin.java:196) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.LoopJoin.computeNext(LoopJoin.java:25) ~[stardog-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:143) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:130) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.LoopJoin.computeNext(LoopJoin.java:196) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.LoopJoin.computeNext(LoopJoin.java:25) ~[stardog-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:143) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:130) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.SingleProjectionOp.computeNext(SingleProjectionOp.java:83) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.SingleProjectionOp.computeNext(SingleProjectionOp.java:33) ~[stardog-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:143) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:130) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.LazyUnsortedGroupify$1.computeNext(GroupifyAlgorithms.java:139) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.LazyUnsortedGroupify$1.computeNext(GroupifyAlgorithms.java:130) ~[stardog-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:143) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:130) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.AbstractGroupOp.computeNext(AbstractGroupOp.java:141) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.AbstractGroupOp.computeNext(AbstractGroupOp.java:34) ~[stardog-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:143) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:130) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.DistinctOp.computeNext(DistinctOp.java:53) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.DistinctOp.computeNext(DistinctOp.java:21) ~[stardog-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:143) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:130) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.util.AutoCloseOperator.computeNext(AutoCloseOperator.java:87) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.util.AutoCloseOperator.computeNext(AutoCloseOperator.java:25) ~[stardog-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:143) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:130) ~[stardog-utils-common-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.util.OpBasedBindingSetIteration.computeNext(OpBasedBindingSetIteration.java:110) ~[stardog-4.1.1.jar:?]
at com.complexible.stardog.plan.eval.operator.util.OpBasedBindingSetIteration.computeNext(OpBasedBindingSetIteration.java:34) ~[stardog-4.1.1.jar:?]
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143) ~[guava-18.0.jar:?]
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138) ~[guava-18.0.jar:?]
at com.complexible.common.rdf.query.IteratorAsTupleQueryResult.hasNext(IteratorAsTupleQueryResult.java:77) ~[stardog-utils-rdf-4.1.1.jar:?]
at com.complexible.stardog.protocols.server.ConnectionFinishQueryResult.hasNext(ConnectionFinishQueryResult.java:75) ~[stardog-protocols-spec-server-4.1.1.jar:?]
at com.complexible.stardog.protocols.server.ConnectionFinishQueryResult.next(ConnectionFinishQueryResult.java:91) ~[stardog-protocols-spec-server-4.1.1.jar:?]
at org.openrdf.query.QueryResults.report(QueryResults.java:159) ~[sesame-query-4.0.0.jar:?]
at org.openrdf.query.resultio.QueryResultIO.writeTuple(QueryResultIO.java:449) ~[sesame-queryresultio-api-4.0.0.jar:?]
at com.complexible.stardog.protocols.http.server.io.ResponseBodyEncoders$13.encode(ResponseBodyEncoders.java:468) ~[stardog-protocols-http-server-4.1.1.jar:?]
... 11 more