Error quitting neo4j-shell and shutting down and embedded .db instance after deleting transaction logs

[John Fry]

Hi All,

I ran out of disk space on a machine and this caused my application to crash when running neo4j in an embedded java application.

I then deleted the transaction log files and this helped get the application starting again. 

However, when ever I try to close the DB at the end of the application I get the error shown below in blue.

Also when quitting the neo4j shell it times out after a long time with the following error:

neo4j-sh (?)$ quit

ERROR (-v for expanded information):

Component 'org.neo4j.kernel.NeoStoreDataSource@6cfabefb' failed to stop. Please see attached cause exception.

Any advice on how to repair the situation?

Thanks in advance for any help, John.

Exception in thread "main" org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.NeoStoreDataSource@217e70a9' failed to stop. Please see attached cause exception.

at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.stop(LifeSupport.java:560)

at org.neo4j.kernel.lifecycle.LifeSupport.stopInstances(LifeSupport.java:161)

at org.neo4j.kernel.lifecycle.LifeSupport.stop(LifeSupport.java:143)

at org.neo4j.kernel.impl.transaction.state.DataSourceManager.stop(DataSourceManager.java:132)

at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.stop(LifeSupport.java:552)

at org.neo4j.kernel.lifecycle.LifeSupport.stopInstances(LifeSupport.java:161)

at org.neo4j.kernel.lifecycle.LifeSupport.stop(LifeSupport.java:143)

at org.neo4j.kernel.lifecycle.LifeSupport.shutdown(LifeSupport.java:184)

at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.shutdown(GraphDatabaseFacade.java:285)

at ReflectorDBTransforms.main(Unknown Source)

Suppressed: org.neo4j.kernel.lifecycle.LifecycleException: Failed to transition component 'org.neo4j.kernel.impl.pagecache.PageCacheLifecycle@462eea6c' from STOPPED to SHUTTING_DOWN. Please see attached cause exception

at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.shutdown(LifeSupport.java:591)

at org.neo4j.kernel.lifecycle.LifeSupport.shutdown(LifeSupport.java:199)

... 2 more

Caused by: java.lang.IllegalStateException: Cannot close the PageCache while files are still mapped:

neostore (1 mapping)

neostore.counts.db.a (1 mapping)

neostore.relationshipgroupstore.db (1 mapping)

neostore.schemastore.db (1 mapping)

neostore.labeltokenstore.db (1 mapping)

neostore.labeltokenstore.db.names (1 mapping)

neostore.relationshiptypestore.db (1 mapping)

neostore.relationshiptypestore.db.names (1 mapping)

neostore.relationshipstore.db (1 mapping)

neostore.propertystore.db (1 mapping)

neostore.propertystore.db.arrays (1 mapping)

neostore.propertystore.db.strings (1 mapping)

neostore.propertystore.db.index (1 mapping)

neostore.propertystore.db.index.keys (1 mapping)

neostore.nodestore.db (1 mapping)

neostore.nodestore.db.labels (1 mapping)

at org.neo4j.io.pagecache.impl.muninn.MuninnPageCache.close(MuninnPageCache.java:519)

at org.neo4j.kernel.impl.pagecache.PageCacheLifecycle.shutdown(PageCacheLifecycle.java:42)

at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.shutdown(LifeSupport.java:583)

... 3 more

Caused by: java.lang.IllegalStateException: Cannot rotate in state: rotating

at org.neo4j.kernel.impl.store.kvstore.ProgressiveState.prepareRotation(ProgressiveState.java:42)

at org.neo4j.kernel.impl.store.kvstore.AbstractKeyValueStore$RotationTask.<init>(AbstractKeyValueStore.java:253)

at org.neo4j.kernel.impl.store.kvstore.AbstractKeyValueStore.prepareRotation(AbstractKeyValueStore.java:220)

at org.neo4j.kernel.impl.store.counts.CountsTracker.rotate(CountsTracker.java:147)

at org.neo4j.kernel.impl.store.NeoStores.flush(NeoStores.java:426)

at org.neo4j.kernel.impl.transaction.log.rotation.StoreFlusher.forceEverything(StoreFlusher.java:52)

at org.neo4j.kernel.NeoStoreDataSource.stop(NeoStoreDataSource.java:1205)

at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.stop(LifeSupport.java:552)

... 9 more

[John Fry]

one addition.

One quick addition: the java application will complete and leave many transaction log files behind. When I start neo4j-shell it won't open unless I delete the log files.

[Chris Vest]

Don’t delete transaction logs. They are required for recovery in case of a crash.

Set `dbms.tx_log.rotation.retention_policy` to `false` in neo4j.conf instead. This will make it keep as few logs as possible.

http://neo4j.com/docs/operations-manual/current/#config_dbms.tx_log.rotation.retention_policy

--

Chris Vest

System Engineer, Neo Technology
[ skype: mr.chrisvest, twitter: chvest ]

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[John Fry]

Hi Chris,

thanks. I will make this change.

Is there any way I can run some kind of fix or recovery of the graph.db I currently have. I am still getting the crash listed below when I run the java app or try to quit neo4j-shell.

Thanks, JF