Getting exception when using neo4j - my services stopped running
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zoharix
Jan 7, 2013, 8:37:23 AM1/7/13
to ne...@googlegroups.com
Hi,
I'm working with neo4j enterprise 1.8GA.
Today I started getting the some exceptions (see below).
I'm using java-rest-bindings and neo4j database that runs in server mode.
I'm not using transactions...
I tried to restart the services but they are failing to start due the below exception:
PLEASE HELP!! :-)
(I haven't tried to restart the DB yet)
Thanks,
Zohar
The first exception that I see in the logs is:
org.neo4j.rest.graphdb.RestResultException: Unable to commit transaction at
TransactionFailureException
org.neo4j.kernel.TopLevelTransaction.finish(TopLevelTransaction.java:134)
org.neo4j.cypher.internal.pipes.CommitPipe.createResults(CommitPipe.scala:45)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl$$anonfun$5$$anonfun$apply$3.apply(ExecutionPlanImpl.scala:104)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl$$anonfun$5$$anonfun$apply$3.apply(ExecutionPlanImpl.scala:104)
org.neo4j.cypher.PipeExecutionResult.immutableResult(PipeExecutionResult.scala:37)
org.neo4j.cypher.EagerPipeExecutionResult.<init>(EagerPipeExecutionResult.scala:44)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl$$anonfun$5.apply(ExecutionPlanImpl.scala:104)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl$$anonfun$5.apply(ExecutionPlanImpl.scala:102)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl.execute(ExecutionPlanImpl.scala:34)
org.neo4j.cypher.ExecutionEngine.execute(ExecutionEngine.scala:55)
org.neo4j.cypher.ExecutionEngine.execute(ExecutionEngine.scala:58)
org.neo4j.cypher.javacompat.ExecutionEngine.execute(ExecutionEngine.java:86)
org.neo4j.server.rest.web.CypherService.cypher(CypherService.java:79)
java.lang.reflect.Method.invoke(Method.java:616)
After that one I see:
java.lang.RuntimeException: Error adding element 4565180 shout_id 1409984 to index SHOUTS
at org.neo4j.rest.graphdb.ExecutingRestAPI.addToIndex(ExecutingRestAPI.java:396)
at org.neo4j.rest.graphdb.RestAPIFacade.addToIndex(RestAPIFacade.java:166)
at org.neo4j.rest.graphdb.index.RestIndex.add(RestIndex.java:60)
at com.listnplay.domain.factory.impl.ShoutFactoryImpl.createShout(ShoutFactoryImpl.java:146)
at com.listnplay.crawler.songMiner.tasks.MusicFetcherTask.executeImpl(MusicFetcherTask.java:207)
at com.listnplay.jobs.Task.execute(Task.java:27)
at com.listnplay.crawler.songMiner.SongMiner$TaskRunner.run(SongMiner.java:173)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:679)
and from there I'm getting the following:
org.neo4j.rest.graphdb.RestResultException: Expected to be in a transaction but wasn't at
InternalException
org.neo4j.cypher.internal.pipes.CommitPipe.tx$1(CommitPipe.scala:31)
org.neo4j.cypher.internal.pipes.CommitPipe.createResults(CommitPipe.scala:45)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl$$anonfun$5$$anonfun$apply$3.apply(ExecutionPlanImpl.scala:104)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl$$anonfun$5$$anonfun$apply$3.apply(ExecutionPlanImpl.scala:104)
org.neo4j.cypher.PipeExecutionResult.immutableResult(PipeExecutionResult.scala:37)
org.neo4j.cypher.EagerPipeExecutionResult.<init>(EagerPipeExecutionResult.scala:44)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl$$anonfun$5.apply(ExecutionPlanImpl.scala:104)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl$$anonfun$5.apply(ExecutionPlanImpl.scala:102)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl.execute(ExecutionPlanImpl.scala:34)
org.neo4j.cypher.ExecutionEngine.execute(ExecutionEngine.scala:55)
org.neo4j.cypher.ExecutionEngine.execute(ExecutionEngine.scala:58)
org.neo4j.cypher.javacompat.ExecutionEngine.execute(ExecutionEngine.java:86)
org.neo4j.server.rest.web.CypherService.cypher(CypherService.java:79)
java.lang.reflect.Method.invoke(Method.java:616)
at org.neo4j.rest.graphdb.ExecutingRestAPI.query(ExecutingRestAPI.java:495)
at org.neo4j.rest.graphdb.RestAPIFacade.query(RestAPIFacade.java:233)
at org.neo4j.rest.graphdb.query.RestCypherQueryEngine.query(RestCypherQueryEngine.java:50)
at com.listnplay.neo4j.Neo4jManager.executeCypherQuery(Neo4jManager.java:86)
Also:
org.neo4j.rest.graphdb.RestResultException: Failed to register lock release synchronization hook at
TransactionFailureException
org.neo4j.kernel.impl.core.LockReleaser.addLockToTransaction(LockReleaser.java:326)
org.neo4j.kernel.impl.transaction.LockType$2.unacquire(LockType.java:62)
org.neo4j.kernel.impl.transaction.LockType.unacquire(LockType.java:90)
org.neo4j.kernel.impl.core.NodeManager.acquireTxBoundLock(NodeManager.java:766)
org.neo4j.kernel.impl.core.NodeManager.getNodeForProxy(NodeManager.java:439)
org.neo4j.kernel.InternalAbstractGraphDatabase$4.lookup(InternalAbstractGraphDatabase.java:666)
org.neo4j.kernel.impl.core.NodeProxy.createRelationshipTo(NodeProxy.java:207)
org.neo4j.cypher.internal.commands.CreateRelationshipStartItem.exec(StartItem.scala:115)
org.neo4j.cypher.internal.commands.CreateRelationshipStartItem.exec(StartItem.scala:86)
org.neo4j.cypher.internal.mutation.CreateUniqueAction$$anonfun$runUpdateCommands$2.apply(CreateUniqueAction.scala:107)
org.neo4j.cypher.internal.mutation.CreateUniqueAction$$anonfun$runUpdateCommands$2.apply(CreateUniqueAction.scala:105)
scala.collection.LinearSeqOptimized$class.foldLeft(LinearSeqOptimized.scala:111)
scala.collection.immutable.List.foldLeft(List.scala:45)
org.neo4j.cypher.internal.mutation.CreateUniqueAction.runUpdateCommands(CreateUniqueAction.scala:105)
org.neo4j.cypher.internal.mutation.CreateUniqueAction.tryAgain(CreateUniqueAction.scala:74)
org.neo4j.cypher.internal.mutation.CreateUniqueAction.exec(CreateUniqueAction.scala:50)
org.neo4j.cypher.internal.pipes.ExecuteUpdateCommandsPipe.org$neo4j$cypher$internal$pipes$ExecuteUpdateCommandsPipe$$exec(ExecuteUpdateCommandsPipe.scala:52)
org.neo4j.cypher.internal.pipes.ExecuteUpdateCommandsPipe$$anonfun$org$neo4j$cypher$internal$pipes$ExecuteUpdateCommandsPipe$$executeMutationCommands$1$$anonfun$apply$1.apply(ExecuteUpdateCommandsPipe.scala:43)
org.neo4j.cypher.internal.pipes.ExecuteUpdateCommandsPipe$$anonfun$org$neo4j$cypher$internal$pipes$ExecuteUpdateCommandsPipe$$executeMutationCommands$1$$anonfun$apply$1.apply(ExecuteUpdateCommandsPipe.scala:43)
scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:200)
scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:200)
scala.collection.LinearSeqOptimized$class.foreach(LinearSeqOptimized.scala:59)
scala.collection.immutable.List.foreach(List.scala:45)
scala.collection.TraversableLike$class.flatMap(TraversableLike.scala:200)
scala.collection.immutable.List.flatMap(List.scala:45)
org.neo4j.cypher.internal.pipes.ExecuteUpdateCommandsPipe$$anonfun$org$neo4j$cypher$internal$pipes$ExecuteUpdateCommandsPipe$$executeMutationCommands$1.apply(ExecuteUpdateCommandsPipe.scala:43)
org.neo4j.cypher.internal.pipes.ExecuteUpdateCommandsPipe$$anonfun$org$neo4j$cypher$internal$pipes$ExecuteUpdateCommandsPipe$$executeMutationCommands$1.apply(ExecuteUpdateCommandsPipe.scala:43)
scala.collection.LinearSeqOptimized$class.foldLeft(LinearSeqOptimized.scala:111)
scala.collection.immutable.List.foldLeft(List.scala:45)
org.neo4j.cypher.internal.pipes.ExecuteUpdateCommandsPipe.org$neo4j$cypher$internal$pipes$ExecuteUpdateCommandsPipe$$executeMutationCommands(ExecuteUpdateCommandsPipe.scala:43)
org.neo4j.cypher.internal.pipes.ExecuteUpdateCommandsPipe$$anonfun$createResults$1.apply(ExecuteUpdateCommandsPipe.scala:35)
org.neo4j.cypher.internal.pipes.ExecuteUpdateCommandsPipe$$anonfun$createResults$1.apply(ExecuteUpdateCommandsPipe.scala:34)
scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:200)
scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:200)
scala.collection.LinearSeqOptimized$class.foreach(LinearSeqOptimized.scala:59)
scala.collection.immutable.List.foreach(List.scala:45)
scala.collection.TraversableLike$class.flatMap(TraversableLike.scala:200)
scala.collection.immutable.List.flatMap(List.scala:45)
org.neo4j.cypher.internal.pipes.ExecuteUpdateCommandsPipe.createResults(ExecuteUpdateCommandsPipe.scala:34)
org.neo4j.cypher.internal.pipes.ColumnFilterPipe.createResults(ColumnFilterPipe.scala:39)
org.neo4j.cypher.internal.pipes.CommitPipe.createResults(CommitPipe.scala:36)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl$$anonfun$5$$anonfun$apply$3.apply(ExecutionPlanImpl.scala:104)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl$$anonfun$5$$anonfun$apply$3.apply(ExecutionPlanImpl.scala:104)
org.neo4j.cypher.PipeExecutionResult.immutableResult(PipeExecutionResult.scala:37)
org.neo4j.cypher.EagerPipeExecutionResult.<init>(EagerPipeExecutionResult.scala:44)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl$$anonfun$5.apply(ExecutionPlanImpl.scala:104)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl$$anonfun$5.apply(ExecutionPlanImpl.scala:102)
org.neo4j.cypher.internal.executionplan.ExecutionPlanImpl.execute(ExecutionPlanImpl.scala:34)
org.neo4j.cypher.ExecutionEngine.execute(ExecutionEngine.scala:55)
org.neo4j.cypher.ExecutionEngine.execute(ExecutionEngine.scala:58)
org.neo4j.cypher.javacompat.ExecutionEngine.execute(ExecutionEngine.java:86)
org.neo4j.server.rest.web.CypherService.cypher(CypherService.java:79)
java.lang.reflect.Method.invoke(Method.java:616)
at org.neo4j.rest.graphdb.ExecutingRestAPI.query(ExecutingRestAPI.java:495)
at org.neo4j.rest.graphdb.RestAPIFacade.query(RestAPIFacade.java:233)
at org.neo4j.rest.graphdb.query.RestCypherQueryEngine.query(RestCypherQueryEngine.java:50)
at com.listnplay.neo4j.Neo4jManager.executeCypherQuery(Neo4jManager.java:86)
zoharix
Jan 7, 2013, 9:01:26 AM1/7/13
to ne...@googlegroups.com
In messages.log I see:
2013-01-07 10:04:55,053 ERROR [neo4j.txmanager]: Commit failed
java.lang.RuntimeException: java.io.IOException: Broken pipe
at org.neo4j.index.impl.lucene.LuceneDataSource.refreshSearcher(LuceneDataSource.java:494) ~[neo4j-lucene-index-1.8.jar:1.8]
at org.neo4j.index.impl.lucene.LuceneDataSource.refreshSearcherIfNeeded(LuceneDataSource.java:600) ~[neo4j-lucene-index-1.8.jar:1.8]
at org.neo4j.index.impl.lucene.LuceneDataSource.getIndexSearcher(LuceneDataSource.java:555) ~[neo4j-lucene-index-1.8.jar:1.8]
at org.neo4j.index.impl.lucene.CommitContext.ensureWriterInstantiated(CommitContext.java:58) ~[neo4j-lucene-index-1.8.jar:1.8]
at org.neo4j.index.impl.lucene.LuceneCommand$AddCommand.perform(LuceneCommand.java:188) ~[neo4j-lucene-index-1.8.jar:1.8]
at org.neo4j.index.impl.lucene.LuceneTransaction.doCommit(LuceneTransaction.java:285) ~[neo4j-lucene-index-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.xaframework.XaTransaction.commit(XaTransaction.java:319) ~[neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.commit(XaResourceManager.java:482) ~[neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceHelpImpl.commit(XaResourceHelpImpl.java:64) ~[neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.TransactionImpl.doCommit(TransactionImpl.java:550) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:439) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:401) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.TransactionImpl.commit(TransactionImpl.java:119) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.TopLevelTransaction.finish(TopLevelTransaction.java:118) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.server.rest.web.DatabaseActions.addToNodeIndex(DatabaseActions.java:811) [neo4j-server-1.8.jar:1.8]
at org.neo4j.server.rest.web.RestfulGraphDatabase.addToNodeIndex(RestfulGraphDatabase.java:777) [neo4j-server-1.8.jar:1.8]
at sun.reflect.GeneratedMethodAccessor109.invoke(Unknown Source) ~[na:na]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:616) ~[na:1.6.0_24]
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.j
ava:205) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1469) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1400) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1349) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1339) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:699) [jersey-server-1.9.jar:1.9]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:820) [servlet-api-2.5-20081211.jar:na]
at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:390) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.Server.handle(Server.java:326) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.HttpConnection$RequestHandler.content(HttpConnection.java:943) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:843) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:218) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:410) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582) [jetty-util-6.1.25.jar:6.1.25]
Caused by: java.io.IOException: Broken pipe
at java.io.RandomAccessFile.writeBytes(Native Method) ~[na:1.6.0_24]
at java.io.RandomAccessFile.write(RandomAccessFile.java:499) ~[na:1.6.0_24]
at org.apache.lucene.store.FSDirectory$FSIndexOutput.flushBuffer(FSDirectory.java:448) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.store.BufferedIndexOutput.flushBuffer(BufferedIndexOutput.java:99) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.store.BufferedIndexOutput.flush(BufferedIndexOutput.java:88) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.store.BufferedIndexOutput.close(BufferedIndexOutput.java:113) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.store.FSDirectory$FSIndexOutput.close(FSDirectory.java:458) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.util.IOUtils.close(IOUtils.java:141) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.index.FieldsWriter.close(FieldsWriter.java:127) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.index.StoredFieldsWriter.flush(StoredFieldsWriter.java:52) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.index.DocFieldProcessor.flush(DocFieldProcessor.java:59) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.index.DocumentsWriter.flush(DocumentsWriter.java:581) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.index.IndexWriter.doFlush(IndexWriter.java:3623) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.index.IndexWriter.flush(IndexWriter.java:3588) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.index.IndexWriter.getReader(IndexWriter.java:452) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.index.IndexWriter.getReader(IndexWriter.java:401) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.index.DirectoryReader.doOpenFromWriter(DirectoryReader.java:428) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.index.DirectoryReader.doOpenIfChanged(DirectoryReader.java:448) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.index.DirectoryReader.doOpenIfChanged(DirectoryReader.java:391) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.index.DirectoryReader.doOpenIfChanged(DirectoryReader.java:407) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.apache.lucene.index.IndexReader.openIfChanged(IndexReader.java:620) ~[lucene-core-3.5.0.jar:3.5.0 1204988 - simon - 2011-11-22 14:46:51]
at org.neo4j.index.impl.lucene.LuceneDataSource.refreshSearcher(LuceneDataSource.java:483) ~[neo4j-lucene-index-1.8.jar:1.8]
... 48 common frames omitted
2013-01-07 10:04:55,156 ERROR [neo4j.txmanager]: Unable to rollback transaction. Some resources may be commited others not. Neo4j kernel should be SHUTDOWN for resource maintance and transaction recovery ---->
javax.transaction.xa.XAException: Transaction already started commit
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.rollback(XaResourceManager.java:525) ~[neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceHelpImpl.rollback(XaResourceHelpImpl.java:111) ~[neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.TransactionImpl.doRollback(TransactionImpl.java:567) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:464) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:401) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.TransactionImpl.commit(TransactionImpl.java:119) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.TopLevelTransaction.finish(TopLevelTransaction.java:118) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.server.rest.web.DatabaseActions.addToNodeIndex(DatabaseActions.java:811) [neo4j-server-1.8.jar:1.8]
at org.neo4j.server.rest.web.RestfulGraphDatabase.addToNodeIndex(RestfulGraphDatabase.java:777) [neo4j-server-1.8.jar:1.8]
at sun.reflect.GeneratedMethodAccessor109.invoke(Unknown Source) ~[na:na]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:616) ~[na:1.6.0_24]
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1469) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1400) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1349) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1339) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:699) [jersey-server-1.9.jar:1.9]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:820) [servlet-api-2.5-20081211.jar:na]
at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:390) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.Server.handle(Server.java:326) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.HttpConnection$RequestHandler.content(HttpConnection.java:943) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:843) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:218) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:410) [jetty-6.1.25.jar:6.1.25]
at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582) [jetty-util-6.1.25.jar:6.1.25]
2013-01-07 10:04:55,157 ERROR [neo4j.txmanager]: setting TM not OK
javax.transaction.xa.XAException: Transaction already started commit
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.rollback(XaResourceManager.java:525) ~[neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceHelpImpl.rollback(XaResourceHelpImpl.java:111) ~[neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.TransactionImpl.doRollback(TransactionImpl.java:567) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:464) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:401) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.TransactionImpl.commit(TransactionImpl.java:119) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.TopLevelTransaction.finish(TopLevelTransaction.java:118) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.server.rest.web.DatabaseActions.addToNodeIndex(DatabaseActions.java:811) [neo4j-server-1.8.jar:1.8]
at org.neo4j.server.rest.web.RestfulGraphDatabase.addToNodeIndex(RestfulGraphDatabase.java:777) [neo4j-server-1.8.jar:1.8]
at sun.reflect.GeneratedMethodAccessor109.invoke(Unknown Source) ~[na:na]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.6.0_24]
at java.lang.reflect.Method.invoke(Method.java:616) ~[na:1.6.0_24]
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1469) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1400) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1349) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1339) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537) [jersey-server-1.9.jar:1.9]
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:699) [jersey-server-1.9.jar:1.9]
zoharix
Jan 7, 2013, 9:12:41 AM1/7/13
to ne...@googlegroups.com
It seems that restart solved the issue but I wonder if it could be fixed without since I intend to use it in production..
On Monday, January 7, 2013 3:37:23 PM UTC+2, zoharix wrote:
On Monday, January 7, 2013 3:37:23 PM UTC+2, zoharix wrote:
Peter Neubauer
Jan 7, 2013, 9:39:01 AM1/7/13
to Neo4j User
Zohar,
do you have that database arounD for analysis somEwhere? Also, can you
please upgrade to 1.8.1 as the latest stable release?
/peter
Cheers,
/peter neubauer
G: neubauer.peter
S: peter.neubauer
P: +46 704 106975
L: http://www.linkedin.com/in/neubauer
T: @peterneubauer
Neo4j 1.8 GA - http://www.dzone.com/links/neo4j_18_release_fluent_graph_literacy.html
> --
>
>
do you have that database arounD for analysis somEwhere? Also, can you
please upgrade to 1.8.1 as the latest stable release?
/peter
Cheers,
/peter neubauer
G: neubauer.peter
S: peter.neubauer
P: +46 704 106975
L: http://www.linkedin.com/in/neubauer
T: @peterneubauer
Neo4j 1.8 GA - http://www.dzone.com/links/neo4j_18_release_fluent_graph_literacy.html
>
>
Jacob Hansson
Jan 7, 2013, 9:52:14 AM1/7/13
to ne...@googlegroups.com
This is a known issue, where the OS fails, for one reason or another, to write to disk. This state means the database has no other option than to bail out, since we don't know what has been written and what has not.
In newer versions of Neo4j (eg. 1.9.x) we will be more resilient against this, the database will attempt a recovery automatically. If successful, the effect will be the same as if the user had restarted the database, except the impact on production is much smaller (a few ms to maybe a few seconds). Requests that come into the database during recovery will queue up and be handled once the database is back in a safe state, assuming the issue with writing to disk is resolved. If the database continues to be unable to talk to the harddrive, it will shut down.
So, in short: We see this once or twice a year, and 1.9.x has fixes that should be enough to resolve the issue.
/jake
zoharix
Jan 7, 2013, 1:00:33 PM1/7/13
to ne...@googlegroups.com
Peter and Jacob, Thanks for the reply.
I don't have database for analysis, sorry.
I will upgrade to 1.8.1, waiting for 1.9 :-)
Thanks again,
Zohar
Zohar Aharoni
Jan 8, 2013, 5:54:40 AM1/8/13
to ne...@googlegroups.com
I've upgraded to 1.8.1.
In the log file I see the following message:
WARNING: Could not lock User prefs. Unix error code 2.
Jan 8, 2013 10:54:45 AM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jan 8, 2013 10:55:15 AM java.util.prefs.FileSystemPreferences checkLockFile0ErrorCode
Peter Neubauer
Jan 8, 2013, 7:05:12 AM1/8/13
to Neo4j User
This looks like some Unix permission problem. As what user is the
process running, and in what directory?
/peter
Cheers,
/peter neubauer
G: neubauer.peter
S: peter.neubauer
P: +46 704 106975
L: http://www.linkedin.com/in/neubauer
T: @peterneubauer
Neo4j 1.8 GA - http://www.dzone.com/links/neo4j_18_release_fluent_graph_literacy.html
> --
>
>
process running, and in what directory?
/peter
Cheers,
/peter neubauer
G: neubauer.peter
S: peter.neubauer
P: +46 704 106975
L: http://www.linkedin.com/in/neubauer
T: @peterneubauer
Neo4j 1.8 GA - http://www.dzone.com/links/neo4j_18_release_fluent_graph_literacy.html
>
>
Zohar Aharoni
Jan 8, 2013, 7:19:10 AM1/8/13
to ne...@googlegroups.com
It is running under user neo4j
I have a symbolic link /var/lib/neo4j that points to /mnt/storage/neo4j/neo4j-enterprise-1.8.1/
--
Peter Neubauer
Jan 8, 2013, 7:23:42 AM1/8/13
to Neo4j User
I think there is a problem having write or lock permissions for the
Java Preferences location, probably related to this?
http://stackoverflow.com/questions/6211048/preferences-systems-tries-to-write-a-lock-file-at-a-location-where-normal-user
/peter
Cheers,
/peter neubauer
G: neubauer.peter
S: peter.neubauer
P: +46 704 106975
L: http://www.linkedin.com/in/neubauer
T: @peterneubauer
Neo4j 1.8 GA - http://www.dzone.com/links/neo4j_18_release_fluent_graph_literacy.html
> --
>
>
Java Preferences location, probably related to this?
http://stackoverflow.com/questions/6211048/preferences-systems-tries-to-write-a-lock-file-at-a-location-where-normal-user
/peter
Cheers,
/peter neubauer
G: neubauer.peter
S: peter.neubauer
P: +46 704 106975
L: http://www.linkedin.com/in/neubauer
T: @peterneubauer
Neo4j 1.8 GA - http://www.dzone.com/links/neo4j_18_release_fluent_graph_literacy.html
>
>
Zohar Aharoni
Jan 8, 2013, 7:39:37 AM1/8/13
to ne...@googlegroups.com
I think that you're right.
So, should I run neo4j server as root? what is the best practice?
--
Peter Neubauer
Feb 8, 2013, 11:05:47 AM2/8/13
to Neo4j User
Well,
normally you have a special user for your services that can access these files and the ports but not much else.
/peter
Cheers,
/peter neubauer
G: neubauer.peter
S: peter.neubauer
P: +46 704 106975
L: http://www.linkedin.com/in/neubauer
T: @peterneubauer
Neo4j 1.8 GA - http://www.dzone.com/links/neo4j_18_release_fluent_graph_literacy.html
--
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