Invalid state exception

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Håvard Ottestad

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Jan 21, 2017, 3:42:11 AM1/21/17
to sta...@clarkparsia.com
Hi

Did a big import of data to stardog during the night and woke up to a very slow stardog with a lot of the following errors in the logs and no writes succeeding.









ERROR 2017-01-21 09:32:09,205 [Stardog.Executor-17777] com.complexible.tx.api.impl.DefaultTransaction:computePrepareResult(489): There was a fatal failure during preparation of 8bb0ecc9-0bac-4f5d-9e70-fd01ee889e37


java.lang.IllegalStateException: Invalid state:  [READABLE]


        at com.google.common.base.Preconditions.checkState(Preconditions.java:197) ~[guava-18.0.jar:?]


        at com.complexible.stardog.index.disk.btree.impl.BPlusTreeImpl.copy(BPlusTreeImpl.java:135) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.index.disk.btree.impl.BPlusTreeImpl.copy(BPlusTreeImpl.java:68) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.index.TernaryIndexImpl.copy(TernaryIndexImpl.java:32) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.index.TernaryIndexImpl.copy(TernaryIndexImpl.java:22) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.index.AbstractIndexData.<init>(AbstractIndexData.java:83) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.index.SingletonIndexData.<init>(SingletonIndexData.java:35) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.index.disk.DiskIndexData.<init>(DiskIndexData.java:63) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.index.disk.DiskIndexData.copy(DiskIndexData.java:136) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.index.disk.DiskIndexData.copy(DiskIndexData.java:39) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.index.AggregateIndexData.mergeDifferentialIndexes(AggregateIndexData.java:99) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.index.AggregateIndexData.update(AggregateIndexData.java:246) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.index.IndexWriterDataMapImpl.applyChanges(IndexWriterDataMapImpl.java:241) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.index.IndexWriterImpl.prepare(IndexWriterImpl.java:208) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.index.impl.DelegatingIndexWriter.prepare(DelegatingIndexWriter.java:140) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.index.ConnectableIndexRWConnectionImpl$TxStateNotifyingIndexWriter.prepare(ConnectableIndexRWConnectionImpl.java:822) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.index.ConnectableIndexRWConnectionImpl$IndexResourceTransaction.prepare(ConnectableIndexRWConnectionImpl.java:564) ~[stardog-4.2.2.jar:?]


        at com.complexible.tx.api.BaseResourceTransaction.prepare(BaseResourceTransaction.java:187) ~[stardog-4.2.2.jar:?]


        at com.complexible.tx.api.impl.DefaultTransaction.computePrepareResult(DefaultTransaction.java:473) ~[stardog-4.2.2.jar:?]


        at com.complexible.tx.api.impl.DefaultTransaction.runPreparePhase(DefaultTransaction.java:439) ~[stardog-4.2.2.jar:?]


        at com.complexible.tx.api.impl.DefaultTransaction.commit(DefaultTransaction.java:330) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.DatabaseConnectionImpl.commit(DatabaseConnectionImpl.java:406) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.DatabaseImpl$DBConnectionWrapper.commit(DatabaseImpl.java:1401) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.DelegatingDatabaseConnection.commit(DelegatingDatabaseConnection.java:279) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.StardogKernel$KernelDbConnection.commit(StardogKernel.java:2767) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.DelegatingDatabaseConnection.commit(DelegatingDatabaseConnection.java:279) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.StardogKernel$NotifyingDatabaseConnection.commit(StardogKernel.java:3035) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.protocols.server.SPECServerFunction.commitTx(SPECServerFunction.java:376) ~[stardog-protocols-spec-server-4.2.2.jar:?]


        at com.complexible.stardog.protocols.server.SPECServerFunction.handleMessage(SPECServerFunction.java:167) ~[stardog-protocols-spec-server-4.2.2.jar:?]


        at com.complexible.common.protocols.server.rpc.ServerHandler.lambda$handleMessage$1(ServerHandler.java:337) ~[stardog-protocols-api-server-4.2.2.jar:?]


        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_92-internal]


        at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_92-internal]


        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_92-internal]


        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_92-internal]


        at java.lang.Thread.run(Thread.java:745) [?:1.8.0_92-internal]


ERROR 2017-01-21 09:32:09,206 [Stardog.Executor-17777] com.complexible.stardog.db.DatabaseConnectionImpl:commit(415): There was an error committing the transaction, all changes were rolled back successfully


com.complexible.tx.api.HeuristicRollbackException: There was a fatal failure during preparation of 8bb0ecc9-0bac-4f5d-9e70-fd01ee889e37 Invalid state:  [READABLE]


        at com.complexible.tx.api.impl.DefaultTransaction.runPreparePhase(DefaultTransaction.java:444) ~[stardog-4.2.2.jar:?]


        at com.complexible.tx.api.impl.DefaultTransaction.commit(DefaultTransaction.java:330) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.DatabaseConnectionImpl.commit(DatabaseConnectionImpl.java:406) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.DatabaseImpl$DBConnectionWrapper.commit(DatabaseImpl.java:1401) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.DelegatingDatabaseConnection.commit(DelegatingDatabaseConnection.java:279) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.StardogKernel$KernelDbConnection.commit(StardogKernel.java:2767) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.DelegatingDatabaseConnection.commit(DelegatingDatabaseConnection.java:279) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.StardogKernel$NotifyingDatabaseConnection.commit(StardogKernel.java:3035) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.protocols.server.SPECServerFunction.commitTx(SPECServerFunction.java:376) ~[stardog-protocols-spec-server-4.2.2.jar:?]


        at com.complexible.stardog.protocols.server.SPECServerFunction.handleMessage(SPECServerFunction.java:167) ~[stardog-protocols-spec-server-4.2.2.jar:?]


        at com.complexible.common.protocols.server.rpc.ServerHandler.lambda$handleMessage$1(ServerHandler.java:337) ~[stardog-protocols-api-server-4.2.2.jar:?]


        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_92-internal]


        at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_92-internal]


        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_92-internal]


        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_92-internal]


        at java.lang.Thread.run(Thread.java:745) [?:1.8.0_92-internal]


ERROR 2017-01-21 09:32:09,206 [Stardog.Executor-17777] com.complexible.common.protocols.server.rpc.ServerHandler:exceptionCaught(428): exceptionCaughtServerHandler


com.complexible.stardog.db.DatabaseException: There was a fatal failure during preparation of 8bb0ecc9-0bac-4f5d-9e70-fd01ee889e37 Invalid state:  [READABLE]


        at com.complexible.stardog.db.DatabaseConnectionImpl.commit(DatabaseConnectionImpl.java:416) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.DatabaseImpl$DBConnectionWrapper.commit(DatabaseImpl.java:1401) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.DelegatingDatabaseConnection.commit(DelegatingDatabaseConnection.java:279) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.StardogKernel$KernelDbConnection.commit(StardogKernel.java:2767) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.DelegatingDatabaseConnection.commit(DelegatingDatabaseConnection.java:279) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.StardogKernel$NotifyingDatabaseConnection.commit(StardogKernel.java:3035) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.protocols.server.SPECServerFunction.commitTx(SPECServerFunction.java:376) ~[stardog-protocols-spec-server-4.2.2.jar:?]


        at com.complexible.stardog.protocols.server.SPECServerFunction.handleMessage(SPECServerFunction.java:167) ~[stardog-protocols-spec-server-4.2.2.jar:?]


        at com.complexible.common.protocols.server.rpc.ServerHandler.lambda$handleMessage$1(ServerHandler.java:337) ~[stardog-protocols-api-server-4.2.2.jar:?]


        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_92-internal]


        at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_92-internal]


        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_92-internal]


        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_92-internal]


        at java.lang.Thread.run(Thread.java:745) [?:1.8.0_92-internal]


Caused by: com.complexible.tx.api.HeuristicRollbackException: There was a fatal failure during preparation of 8bb0ecc9-0bac-4f5d-9e70-fd01ee889e37 Invalid state:  [READABLE]


        at com.complexible.tx.api.impl.DefaultTransaction.runPreparePhase(DefaultTransaction.java:444) ~[stardog-4.2.2.jar:?]


        at com.complexible.tx.api.impl.DefaultTransaction.commit(DefaultTransaction.java:330) ~[stardog-4.2.2.jar:?]


        at com.complexible.stardog.db.DatabaseConnectionImpl.commit(DatabaseConnectionImpl.java:406) ~[stardog-4.2.2.jar:?]


        ... 13 more



Restarting stardog seems to have fixed the errors. 

Cheers,
Håvard M. Ottestad
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