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 <michael.hun...@neotechnology.com>
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(Life
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:
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 >
