Neo4j failed to start under Docker: "Already closed exception"
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Alan Robertson
Sep 1, 2016, 1:11:37 PM9/1/16
to Neo4J
Hi,
I've been having trouble with getting Neo4j to start in a docker image. This image was produced by a Dockerfile which built my software and installed and ran Neo4j and my tests without any issues. But when I try and start the resulting image, Neo4j declines to start for mysterious reasons. The logs from trying to start it are below:
NEO4J_CONF=/etc/neo4j /usr/share/neo4j/bin/neo4j console
Starting Neo4j.
2016-09-01 16:53:40.342+0000 INFO Starting...
2016-09-01 16:53:40.613+0000 INFO Bolt enabled on localhost:7687.
2016-09-01 16:53:43.864+0000 ERROR Failed to start Neo4j: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@1377f3c' was successfully initialized, but failed to start. Please see attached cause exception. Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@1377f3c' was successfully initialized, but failed to start. Please see attached cause exception.
org.neo4j.server.ServerStartupException: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@1377f3c' was successfully initialized, but failed to start. Please see attached cause exception.
at org.neo4j.server.exception.ServerStartupErrors.translateToServerStartupError(ServerStartupErrors.java:68)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:217)
at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:90)
at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:67)
at org.neo4j.server.CommunityEntryPoint.main(CommunityEntryPoint.java:28)
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.server.database.LifecycleManagingDatabase@1377f3c' was successfully initialized, but failed to start. Please see attached cause exception.
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:444)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:107)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:189)
... 3 more
Caused by: java.lang.RuntimeException: Error starting org.neo4j.kernel.impl.factory.CommunityFacadeFactory, /var/lib/neo4j/data/databases/graph.db
at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:144)
at org.neo4j.kernel.impl.factory.CommunityFacadeFactory.newFacade(CommunityFacadeFactory.java:40)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:108)
at org.neo4j.server.CommunityNeoServer.lambda$static$0(CommunityNeoServer.java:55)
at org.neo4j.server.database.LifecycleManagingDatabase.start(LifecycleManagingDatabase.java:89)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:434)
... 5 more
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.recovery.Recovery@5ddaeea7' failed to initialize. Please see attached cause exception.
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:416)
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:62)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:98)
at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:511)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:434)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:107)
at org.neo4j.kernel.impl.transaction.state.DataSourceManager.start(DataSourceManager.java:99)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:434)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:107)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:140)
... 10 more
Caused by: org.apache.lucene.store.AlreadyClosedException: this IndexReader is closed
at org.apache.lucene.index.IndexReader.ensureOpen(IndexReader.java:274)
at org.apache.lucene.index.CompositeReader.getContext(CompositeReader.java:101)
at org.apache.lucene.index.CompositeReader.getContext(CompositeReader.java:55)
at org.apache.lucene.index.IndexReader.leaves(IndexReader.java:438)
at org.apache.lucene.index.MultiFields.getFields(MultiFields.java:63)
at org.apache.lucene.index.MultiFields.getTerms(MultiFields.java:120)
at org.apache.lucene.search.IndexSearcher.collectionStatistics(IndexSearcher.java:964)
at org.apache.lucene.search.TermQuery$TermWeight.<init>(TermQuery.java:65)
at org.apache.lucene.search.TermQuery.createWeight(TermQuery.java:198)
at org.apache.lucene.search.IndexSearcher.createWeight(IndexSearcher.java:904)
at org.apache.lucene.search.IndexSearcher.createNormalizedWeight(IndexSearcher.java:887)
at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:535)
at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:744)
at org.apache.lucene.search.IndexSearcher.searchAfter(IndexSearcher.java:460)
at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:489)
at org.neo4j.index.impl.lucene.legacy.LuceneDataSource.findDocument(LuceneDataSource.java:436)
at org.neo4j.index.impl.lucene.legacy.CommitContext.getDocument(CommitContext.java:71)
at org.neo4j.index.impl.lucene.legacy.LuceneCommandApplier.visitIndexAddCommand(LuceneCommandApplier.java:88)
at org.neo4j.index.impl.lucene.legacy.LuceneCommandApplier.visitIndexAddNodeCommand(LuceneCommandApplier.java:62)
at org.neo4j.kernel.impl.api.LegacyIndexTransactionApplier.visitIndexAddNodeCommand(LegacyIndexTransactionApplier.java:166)
at org.neo4j.kernel.impl.index.IndexCommand$AddNodeCommand.handle(IndexCommand.java:233)
at org.neo4j.kernel.impl.api.TransactionApplierFacade.visit(TransactionApplierFacade.java:61)
at org.neo4j.kernel.impl.api.TransactionApplierFacade.visit(TransactionApplierFacade.java:35)
at org.neo4j.kernel.impl.transaction.log.PhysicalTransactionRepresentation.accept(PhysicalTransactionRepresentation.java:69)
at org.neo4j.kernel.impl.api.TransactionToApply.accept(TransactionToApply.java:108)
at org.neo4j.kernel.impl.storageengine.impl.recordstorage.RecordStorageEngine.apply(RecordStorageEngine.java:341)
at org.neo4j.kernel.impl.transaction.state.RecoveryVisitor.applyQueue(RecoveryVisitor.java:87)
at org.neo4j.kernel.impl.api.TransactionQueue.empty(TransactionQueue.java:67)
at org.neo4j.kernel.impl.transaction.state.RecoveryVisitor.close(RecoveryVisitor.java:93)
at org.neo4j.kernel.impl.transaction.log.LogFileRecoverer.visit(LogFileRecoverer.java:80)
at org.neo4j.kernel.impl.transaction.log.LogFileRecoverer.visit(LogFileRecoverer.java:30)
at org.neo4j.kernel.recovery.Recovery.init(Recovery.java:86)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:406)
I've been having trouble with getting Neo4j to start in a docker image. This image was produced by a Dockerfile which built my software and installed and ran Neo4j and my tests without any issues. But when I try and start the resulting image, Neo4j declines to start for mysterious reasons. The logs from trying to start it are below:
NEO4J_CONF=/etc/neo4j /usr/share/neo4j/bin/neo4j console
Starting Neo4j.
2016-09-01 16:53:40.342+0000 INFO Starting...
2016-09-01 16:53:40.613+0000 INFO Bolt enabled on localhost:7687.
2016-09-01 16:53:43.864+0000 ERROR Failed to start Neo4j: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@1377f3c' was successfully initialized, but failed to start. Please see attached cause exception. Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@1377f3c' was successfully initialized, but failed to start. Please see attached cause exception.
org.neo4j.server.ServerStartupException: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@1377f3c' was successfully initialized, but failed to start. Please see attached cause exception.
at org.neo4j.server.exception.ServerStartupErrors.translateToServerStartupError(ServerStartupErrors.java:68)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:217)
at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:90)
at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:67)
at org.neo4j.server.CommunityEntryPoint.main(CommunityEntryPoint.java:28)
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.server.database.LifecycleManagingDatabase@1377f3c' was successfully initialized, but failed to start. Please see attached cause exception.
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:444)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:107)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:189)
... 3 more
Caused by: java.lang.RuntimeException: Error starting org.neo4j.kernel.impl.factory.CommunityFacadeFactory, /var/lib/neo4j/data/databases/graph.db
at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:144)
at org.neo4j.kernel.impl.factory.CommunityFacadeFactory.newFacade(CommunityFacadeFactory.java:40)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:108)
at org.neo4j.server.CommunityNeoServer.lambda$static$0(CommunityNeoServer.java:55)
at org.neo4j.server.database.LifecycleManagingDatabase.start(LifecycleManagingDatabase.java:89)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:434)
... 5 more
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.recovery.Recovery@5ddaeea7' failed to initialize. Please see attached cause exception.
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:416)
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:62)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:98)
at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:511)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:434)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:107)
at org.neo4j.kernel.impl.transaction.state.DataSourceManager.start(DataSourceManager.java:99)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:434)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:107)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:140)
... 10 more
Caused by: org.apache.lucene.store.AlreadyClosedException: this IndexReader is closed
at org.apache.lucene.index.IndexReader.ensureOpen(IndexReader.java:274)
at org.apache.lucene.index.CompositeReader.getContext(CompositeReader.java:101)
at org.apache.lucene.index.CompositeReader.getContext(CompositeReader.java:55)
at org.apache.lucene.index.IndexReader.leaves(IndexReader.java:438)
at org.apache.lucene.index.MultiFields.getFields(MultiFields.java:63)
at org.apache.lucene.index.MultiFields.getTerms(MultiFields.java:120)
at org.apache.lucene.search.IndexSearcher.collectionStatistics(IndexSearcher.java:964)
at org.apache.lucene.search.TermQuery$TermWeight.<init>(TermQuery.java:65)
at org.apache.lucene.search.TermQuery.createWeight(TermQuery.java:198)
at org.apache.lucene.search.IndexSearcher.createWeight(IndexSearcher.java:904)
at org.apache.lucene.search.IndexSearcher.createNormalizedWeight(IndexSearcher.java:887)
at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:535)
at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:744)
at org.apache.lucene.search.IndexSearcher.searchAfter(IndexSearcher.java:460)
at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:489)
at org.neo4j.index.impl.lucene.legacy.LuceneDataSource.findDocument(LuceneDataSource.java:436)
at org.neo4j.index.impl.lucene.legacy.CommitContext.getDocument(CommitContext.java:71)
at org.neo4j.index.impl.lucene.legacy.LuceneCommandApplier.visitIndexAddCommand(LuceneCommandApplier.java:88)
at org.neo4j.index.impl.lucene.legacy.LuceneCommandApplier.visitIndexAddNodeCommand(LuceneCommandApplier.java:62)
at org.neo4j.kernel.impl.api.LegacyIndexTransactionApplier.visitIndexAddNodeCommand(LegacyIndexTransactionApplier.java:166)
at org.neo4j.kernel.impl.index.IndexCommand$AddNodeCommand.handle(IndexCommand.java:233)
at org.neo4j.kernel.impl.api.TransactionApplierFacade.visit(TransactionApplierFacade.java:61)
at org.neo4j.kernel.impl.api.TransactionApplierFacade.visit(TransactionApplierFacade.java:35)
at org.neo4j.kernel.impl.transaction.log.PhysicalTransactionRepresentation.accept(PhysicalTransactionRepresentation.java:69)
at org.neo4j.kernel.impl.api.TransactionToApply.accept(TransactionToApply.java:108)
at org.neo4j.kernel.impl.storageengine.impl.recordstorage.RecordStorageEngine.apply(RecordStorageEngine.java:341)
at org.neo4j.kernel.impl.transaction.state.RecoveryVisitor.applyQueue(RecoveryVisitor.java:87)
at org.neo4j.kernel.impl.api.TransactionQueue.empty(TransactionQueue.java:67)
at org.neo4j.kernel.impl.transaction.state.RecoveryVisitor.close(RecoveryVisitor.java:93)
at org.neo4j.kernel.impl.transaction.log.LogFileRecoverer.visit(LogFileRecoverer.java:80)
at org.neo4j.kernel.impl.transaction.log.LogFileRecoverer.visit(LogFileRecoverer.java:30)
at org.neo4j.kernel.recovery.Recovery.init(Recovery.java:86)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:406)
--
Alan
Robertson / CTO
Al...@AssimilationSystems.com / +1 303.947.7999
Assimilation Systems
Limited
http://AssimilationSystems.com
Alan Robertson
Sep 22, 2016, 5:40:00 PM9/22/16
to ne...@googlegroups.com
It looks like this is some kind of bug
related to Docker and apparmor. Disabling apparmor makes it go
away...
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Alan Robertson
Sep 22, 2016, 5:47:34 PM9/22/16
to ne...@googlegroups.com
Wrong. I didn't test what I thought I
did - it's still broken - Sigh...
For some reason I didn't have the initial failure messages in the logs below - but here are some additional messages.
[o.n.k.i.s.f.RecordFormatSelector] Selected RecordFormat:StandardV3_0[v0.A.7] record format from store /var/lib/neo4j/data/databases/graph.db
[o.n.k.i.s.f.RecordFormatSelector] Format not configured. Selected format from the store: RecordFormat:StandardV3_0[v0.A.7]
[o.n.k.NeoStoreDataSource] Recovery required from position LogPosition{logVersion=0, byteOffset=362783}
ERROR [o.n.k.i.DatabaseHealth] Database panic: Database has encountered some problem, please perform necessary action (tx recovery/restart) this IndexReader is closed
For some reason I didn't have the initial failure messages in the logs below - but here are some additional messages.
[o.n.k.i.s.f.RecordFormatSelector] Selected RecordFormat:StandardV3_0[v0.A.7] record format from store /var/lib/neo4j/data/databases/graph.db
[o.n.k.i.s.f.RecordFormatSelector] Format not configured. Selected format from the store: RecordFormat:StandardV3_0[v0.A.7]
[o.n.k.NeoStoreDataSource] Recovery required from position LogPosition{logVersion=0, byteOffset=362783}
ERROR [o.n.k.i.DatabaseHealth] Database panic: Database has encountered some problem, please perform necessary action (tx recovery/restart) this IndexReader is closed
Alan Robertson
Sep 22, 2016, 5:56:02 PM9/22/16
to ne...@googlegroups.com, Michael Hunger
But I know how to work around it for my
particular case...
Remove all the files under /var/lib/neo4j/data/databases/graph.db (!)
That seems a little extreme... But I didn't need that data for my particular circumstance - so it works for me.
Presumably someone else will run into circumstances where they will need their data...
-- Alan
Remove all the files under /var/lib/neo4j/data/databases/graph.db (!)
That seems a little extreme... But I didn't need that data for my particular circumstance - so it works for me.
Presumably someone else will run into circumstances where they will need their data...
-- Alan
Lüdicke, Benjamin
Sep 27, 2016, 8:18:13 PM9/27/16
to ne...@googlegroups.com
Ja ist klar. Wird alles über Weihnachten verbraten.
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