AW: Neo4j fails to start with certain kinds of corruption?? WAS: Re: [Neo4j] Neo4j failed to start under Docker: "Already closed exception"
Ja ist klar. Wird alles über Weihnachten verbraten. Von: Alan Robertson [mailto:alan.robertson...@gmail.com] Im Auftrag von Alan Robertson Gesendet: Donnerstag, 22. September 2016 23:56 An: neo4j@googlegroups.com Cc: Michael Hunger Betreff: Neo4j fails to start with certain kinds of corruption?? WAS: Re: [Neo4j] Neo4j failed to start under Docker: "Already closed exception" 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+ INFO Starting... 2016-09-01 16:53:40.613+ INFO Bolt enabled on localhost:7687. 2016-09-01 16:53:43.864+ 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
Neo4j fails to start with certain kinds of corruption?? WAS: Re: [Neo4j] Neo4j failed to start under Docker: "Already closed exception"
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+ INFO Starting... >>> 2016-09-01 16:53:40.613+ INFO Bolt enabled on localhost:7687. >>> 2016-09-01 16:53:43.864+ 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) >>>
Re: [Neo4j] Neo4j failed to start under Docker: "Already closed exception"
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+ INFO Starting... >> 2016-09-01 16:53:40.613+ INFO Bolt enabled on localhost:7687. >> 2016-09-01 16:53:43.864+ 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.
Re: [Neo4j] Neo4j failed to start under Docker: "Already closed exception"
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+ INFO Starting... > 2016-09-01 16:53:40.613+ INFO Bolt enabled on localhost:7687. > 2016-09-01 16:53:43.864+ 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$LifecycleInstance.start(LifeSupp
[Neo4j] Neo4j failed to start under Docker: "Already closed exception"
Hi, I've been having trouble with getting Neo4j to start in a docker image. This image was produced by a Dockerfile which built my software and installed and ran Neo4j and my tests without any issues. But when I try and start the resulting image, Neo4j declines to start for mysterious reasons. The logs from trying to start it are below: NEO4J_CONF=/etc/neo4j /usr/share/neo4j/bin/neo4j console Starting Neo4j. 2016-09-01 16:53:40.342+ INFO Starting... 2016-09-01 16:53:40.613+ INFO Bolt enabled on localhost:7687. 2016-09-01 16:53:43.864+ ERROR Failed to start Neo4j: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@1377f3c' was successfully initialized, but failed to start. Please see attached cause exception. Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@1377f3c' was successfully initialized, but failed to start. Please see attached cause exception. org.neo4j.server.ServerStartupException: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@1377f3c' was successfully initialized, but failed to start. Please see attached cause exception. at org.neo4j.server.exception.ServerStartupErrors.translateToServerStartupError(ServerStartupErrors.java:68) at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:217) at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:90) at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:67) at org.neo4j.server.CommunityEntryPoint.main(CommunityEntryPoint.java:28) Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.server.database.LifecycleManagingDatabase@1377f3c' was successfully initialized, but failed to start. Please see attached cause exception. at org.neo4j.kernel.lifecycle.LifeSupport$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.Index