Facing "org.neo4j.kernel.impl.nioneo.store.UnderlyingStorageException: Unable to load position" at startup of Neo4j server.

[Narendran Thangarajan]

Hi all,

I downloaded the latest version of neo4j database (unix variant) on my ubuntu machine. I set my ulimit to 40000 as suggested in the documentation. When I execute './neo4j start' from the bin folder, I get the following exception in data/graph.db/messages.log. And the server doesn't start. Could you please help me solve this issue?

Please let me know if you need more details.

Stack Trace :

2014-11-27 02:11:43.344+0000 INFO  [o.n.k.i.t.TxManager]: TM new log: tm_tx_log.1

2014-11-27 02:11:43.424+0000 INFO  [o.n.k.i.t.KernelHealth]: Kernel health set to OK

2014-11-27 02:13:50.869+0000 ERROR [o.n.k.i.t.XaDataSourceManager]: Failed when notifying registering listener

org.neo4j.kernel.impl.nioneo.store.UnderlyingStorageException: Unable to load position[1] @[9]

at org.neo4j.kernel.impl.nioneo.store.PersistenceRow.readFullWindow(PersistenceRow.java:162) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.nioneo.store.PersistenceRow$State$1.transition(PersistenceRow.java:114) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.nioneo.store.PersistenceRow.lock(PersistenceRow.java:58) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.nioneo.store.PersistenceWindowPool.acquire(PersistenceWindowPool.java:197) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.nioneo.store.CommonAbstractStore.acquireWindow(CommonAbstractStore.java:546) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.nioneo.store.NeoStore.getRecord(NeoStore.java:553) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.nioneo.store.NeoStore.getRandomNumber(NeoStore.java:434) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource.getRandomIdentifier(NeoStoreXaDataSource.java:654) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.ext.udc.impl.DefaultUdcInformationCollector$1.registeredDataSource(DefaultUdcInformationCollector.java:100) ~[neo4j-udc-2.1.5.jar:na]

at org.neo4j.kernel.impl.transaction.XaDataSourceManager.addDataSourceRegistrationListener(XaDataSourceManager.java:128) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.ext.udc.impl.DefaultUdcInformationCollector.<init>(DefaultUdcInformationCollector.java:92) [neo4j-udc-2.1.5.jar:na]

at org.neo4j.ext.udc.impl.UdcKernelExtension.start(UdcKernelExtension.java:72) [neo4j-udc-2.1.5.jar:na]

at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:507) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.extension.KernelExtensions.start(KernelExtensions.java:119) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:507) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:343) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:59) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.server.database.LifecycleManagingDatabase$1.newGraphDatabase(LifecycleManagingDatabase.java:45) [neo4j-server-2.1.5.jar:2.1.5]

at org.neo4j.server.database.LifecycleManagingDatabase.start(LifecycleManagingDatabase.java:119) [neo4j-server-2.1.5.jar:2.1.5]

at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:167) [neo4j-server-2.1.5.jar:2.1.5]

at org.neo4j.server.Bootstrapper.start(Bootstrapper.java:108) [neo4j-server-2.1.5.jar:2.1.5]

at org.neo4j.server.Bootstrapper.main(Bootstrapper.java:62) [neo4j-server-2.1.5.jar:2.1.5]

Caused by: java.nio.channels.ClosedByInterruptException: null

at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202) ~[na:1.7.0_65]

at sun.nio.ch.FileChannelImpl.readInternal(FileChannelImpl.java:706) ~[na:1.7.0_65]

at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:685) ~[na:1.7.0_65]

at org.neo4j.kernel.impl.nioneo.store.StoreFileChannel.read(StoreFileChannel.java:112) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.nioneo.store.PersistenceRow.readFullWindow(PersistenceRow.java:157) ~[neo4j-kernel-2.1.5.jar:2.1.5]

... 23 common frames omitted

2014-11-27 02:13:50.902+0000 ERROR [o.n.k.i.t.TxManager]: Unable to close tx log[/home/pircnet/software/unix-neo4j/neo4j-community-2.1.5/data/graph.db/tm_tx_log.1]

java.nio.channels.ClosedByInterruptException: null

at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202) ~[na:1.7.0_65]

at sun.nio.ch.FileChannelImpl.writeInternal(FileChannelImpl.java:744) ~[na:1.7.0_65]

at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:724) ~[na:1.7.0_65]

at org.neo4j.kernel.impl.nioneo.store.StoreFileChannel.write(StoreFileChannel.java:51) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.nioneo.store.StoreFileChannel.writeAll(StoreFileChannel.java:72) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.transaction.xaframework.DirectMappedLogBuffer.writeOut(DirectMappedLogBuffer.java:162) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.transaction.xaframework.DirectMappedLogBuffer.force(DirectMappedLogBuffer.java:171) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.transaction.TxLog.close(TxLog.java:166) ~[neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.transaction.TxManager.closeLog(TxManager.java:276) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.impl.transaction.TxManager.stop(TxManager.java:233) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.stop(LifeSupport.java:527) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.lifecycle.LifeSupport.stop(LifeSupport.java:155) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:123) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:343) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:59) [neo4j-kernel-2.1.5.jar:2.1.5]

at org.neo4j.server.database.LifecycleManagingDatabase$1.newGraphDatabase(LifecycleManagingDatabase.java:45) [neo4j-server-2.1.5.jar:2.1.5]

at org.neo4j.server.database.LifecycleManagingDatabase.start(LifecycleManagingDatabase.java:119) [neo4j-server-2.1.5.jar:2.1.5]

at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:167) [neo4j-server-2.1.5.jar:2.1.5]

at org.neo4j.server.Bootstrapper.start(Bootstrapper.java:108) [neo4j-server-2.1.5.jar:2.1.5]

at org.neo4j.server.Bootstrapper.main(Bootstrapper.java:62) [neo4j-server-2.1.5.jar:2.1.5]

2014-11-27 02:13:50.903+0000 INFO  [o.n.k.i.t.TxManager]: TM shutting down

2014-11-27 02:13:50.908+0000 INFO  [o.n.k.i.DiagnosticsManager]: --- STOPPING diagnostics START ---

2014-11-27 02:13:50.908+0000 INFO  [o.n.k.i.DiagnosticsManager]: --- STOPPING diagnostics END ---

2014-11-27 02:13:50.913+0000 ERROR [o.n.k.EmbeddedGraphDatabase]: Startup failed: Component 'org.neo4j.kernel.impl.transaction.XaDataSourceManager@4b9e8b55' failed to stop. Please see attached cause exception.: Component 'org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource@244b9168' failed to stop. Please see attached cause exception.: java.nio.channels.ClosedByInterruptException: null: Component 'org.neo4j.kernel.extension.KernelExtensions@5f594a5f' was successfully initialized, but failed to start. Please see attached cause exception.: Component 'org.neo4j.index.lucene.LuceneKernelExtension@295ebdbf' was successfully initialized, but failed to start. Please see attached cause exception.: Component 'org.neo4j.index.impl.lucene.LuceneDataSource@129ba8ac' was successfully initialized, but failed to start. Please see attached cause exception.: java.nio.channels.ClosedByInterruptException: null

Thanks,

Narendran

[Michael Hunger]

Did you have a previous database there?

Can you check the filesystem permissions?

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[Michael Hunger]

Also could you share your full messages.log and perhaps your database?

Please send it to me personally.

Thanks Michael