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

On 09/22/2016 03:47 PM, Alan Robertson wrote:
> 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*
>
>
> On 09/22/2016 03:39 PM, Alan Robertson wrote:
>> It looks like this is some kind of bug related to Docker and
>> apparmor. Disabling apparmor makes it go away...
>>
>>
>> On 09/01/2016 11:11 AM, Alan Robertson wrote:
>>> 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)

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