Error when beginning a transaction

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Kofi

unread,
Jan 13, 2014, 11:55:22 AM1/13/14
to ne...@googlegroups.com
I am using neo4j 1.9.5 with glassfish 3.1.1


I occasionally(hardly occurs) get this error while beginning a transaction to create a node



org.neo4j.graphdb.TransactionFailureException: Unable to begin transaction
 at org
.neo4j.kernel.AbstractGraphDatabase.beginTx(AbstractGraphDatabase.java:771)
 at org
.neo4j.kernel.TransactionBuilderImpl.begin(TransactionBuilderImpl.java:39)
 at org
.neo4j.kernel.AbstractGraphDatabase.beginTx(AbstractGraphDatabase.java:749)
       
.
       
.
       
.
       
.
at java
.lang.Thread.run(Thread.java:722)
Caused by: javax.transaction.SystemException: TM has encountered some problem, please perform neccesary action (tx recovery/restart)
 at org
.neo4j.kernel.impl.transaction.TxManager.assertTmOk(TxManager.java:358)
 at org
.neo4j.kernel.impl.transaction.TxManager.begin(TxManager.java:335)
 at org
.neo4j.kernel.AbstractGraphDatabase.beginTx(AbstractGraphDatabase.java:766)
 
... 37 more



What could be the cause of the error and any suggestions how it could be resolved

Michael Hunger

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Jan 13, 2014, 8:30:02 PM1/13/14
to ne...@googlegroups.com
Can you share your graph.db/messages.log file for some insight?

Thanks

Michael
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Kofi

unread,
Jan 14, 2014, 7:19:18 AM1/14/14
to ne...@googlegroups.com
Hi below is the logs





2014-01-10 17:16:07.130+0000: GC Monitor: Application threads blocked for an additional 685ms [total block time: 509.525s]
2014-01-10 17:23:29.280+0000: TM error tx commit Failed to commit, transaction rolledback ---> error code was: 0
javax
.transaction.HeuristicRollbackException: Failed to commit, transaction rolledback ---> error code was: 0
 at org
.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:515)
 at org
.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:406)
 at org
.neo4j.kernel.impl.transaction.TransactionImpl.commit(TransactionImpl.java:117)
 at org
.neo4j.kernel.TopLevelTransaction.finish(TopLevelTransaction.java:115)
 at javax
.servlet.http.HttpServlet.service(HttpServlet.java:688)
 at javax
.servlet.http.HttpServlet.service(HttpServlet.java:770)
 at org
.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)
 at org
.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:343)
 at org
.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:217)
 at com
.opensymphony.sitemesh.webapp.SiteMeshFilter.obtainContent(SiteMeshFilter.java:129)
 at com
.opensymphony.sitemesh.webapp.SiteMeshFilter.doFilter(SiteMeshFilter.java:77)
 at org
.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
 at org
.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:217)
 at org
.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:279)
 at org
.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
 at org
.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)
 at org
.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)
 at org
.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)
 at org
.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:331)
 at org
.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)
 at com
.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)
 at com
.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)
 at com
.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)
 at com
.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)
 at com
.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)
 at com
.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)
 at com
.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)
 at com
.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)
 at com
.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)
 at com
.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)
 at com
.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)
 at com
.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)
 at com
.sun.grizzly.ContextTask.run(ContextTask.java:71)
 at com
.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)
 at com
.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)
 at java
.lang.Thread.run(Thread.java:722)
2014-01-10 17:23:29.293+0000: TM error tx commit Failed to commit, transaction rolledback ---> java.nio.BufferOverflowException
javax
.transaction.HeuristicRollbackException: Failed to commit, transaction rolledback ---> java.nio.BufferOverflowException
 at org
.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:521)
 at org
.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:406)
 at org
.neo4j.kernel.impl.transaction.TransactionImpl.commit(TransactionImpl.java:117)
 at org
.neo4j.kernel.TopLevelTransaction.finish(TopLevelTransaction.java:115)
 at javax
.servlet.http.HttpServlet.service(HttpServlet.java:688)
 at javax
.servlet.http.HttpServlet.service(HttpServlet.java:770)
 at org
.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)
 at org
.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:343)
 at org
.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:217)
 at com
.opensymphony.sitemesh.webapp.SiteMeshFilter.obtainContent(SiteMeshFilter.java:129)
 at com
.opensymphony.sitemesh.webapp.SiteMeshFilter.doFilter(SiteMeshFilter.java:77)
 at org
.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
 at org
.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:217)
 at org
.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:279)
 at org
.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
 at org
.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)
 at org
.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)
 at org
.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)
 at org
.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:331)
 at org
.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)
 at com
.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)
 at com
.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)
 at com
.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)
 at com
.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)
 at com
.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)
 at com
.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)
 at com
.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)
 at com
.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)
 at com
.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)
 at com
.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)
 at com
.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)
 at com
.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)
 at com
.sun.grizzly.ContextTask.run(ContextTask.java:71)
 at com
.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)
 at com
.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)
 at java
.lang.Thread.run(Thread.java:722)
Caused by: java.nio.BufferOverflowException
 at java
.nio.Buffer.nextPutIndex(Buffer.java:519)
 at java
.nio.DirectByteBuffer.putLong(DirectByteBuffer.java:787)
 at org
.neo4j.kernel.impl.transaction.xaframework.DirectMappedLogBuffer.putLong(DirectMappedLogBuffer.java:86)
 at org
.neo4j.kernel.impl.nioneo.xa.Command.writePropertyBlock(Command.java:90)
 at org
.neo4j.kernel.impl.nioneo.xa.Command.access$000(Command.java:51)
 at org
.neo4j.kernel.impl.nioneo.xa.Command$PropertyCommand.writeToFile(Command.java:839)
 at org
.neo4j.kernel.impl.transaction.xaframework.LogIoUtils.writeCommand(LogIoUtils.java:255)
 at org
.neo4j.kernel.impl.transaction.xaframework.XaLogicalLog.writeCommand(XaLogicalLog.java:448)
 at org
.neo4j.kernel.impl.transaction.xaframework.XaTransaction.addCommand(XaTransaction.java:242)
 at org
.neo4j.kernel.impl.nioneo.xa.WriteTransaction.doPrepare(WriteTransaction.java:230)
 at org
.neo4j.kernel.impl.transaction.xaframework.XaTransaction.prepare(XaTransaction.java:299)
 at org
.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.commit(XaResourceManager.java:435)
 at org
.neo4j.kernel.impl.transaction.xaframework.XaResourceHelpImpl.commit(XaResourceHelpImpl.java:64)
 at org
.neo4j.kernel.impl.transaction.TransactionImpl.doCommit(TransactionImpl.java:541)
 at org
.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:444)
 
... 39 more
2014-01-10 17:25:12.109+0000: setting TM not OK null
java
.nio.BufferOverflowException
 at java
.nio.Buffer.nextPutIndex(Buffer.java:513)
 at java
.nio.DirectByteBuffer.put(DirectByteBuffer.java:291)
 at org
.neo4j.kernel.impl.transaction.xaframework.DirectMappedLogBuffer.put(DirectMappedLogBuffer.java:65)
 at org
.neo4j.kernel.impl.transaction.xaframework.LogIoUtils.writeStart(LogIoUtils.java:246)
 at org
.neo4j.kernel.impl.transaction.xaframework.XaLogicalLog.writeStartEntry(XaLogicalLog.java:303)
 at org
.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.checkStartWritten(XaResourceManager.java:307)
 at org
.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.rollback(XaResourceManager.java:512)
 at org
.neo4j.kernel.impl.transaction.xaframework.XaResourceHelpImpl.rollback(XaResourceHelpImpl.java:111)
 at org
.neo4j.kernel.impl.transaction.TransactionImpl.doRollback(TransactionImpl.java:558)
 at org
.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:469)
 at org
.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:406)
 at org
.neo4j.kernel.impl.transaction.TransactionImpl.commit(TransactionImpl.java:117)
 at org
.neo4j.kernel.TopLevelTransaction.finish(TopLevelTransaction.java:115)
 at javax
.servlet.http.HttpServlet.service(HttpServlet.java:688)
 at javax
.servlet.http.HttpServlet.service(HttpServlet.java:770)
 at org
.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)
 at org
.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:343)
 at org
.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:217)
 at com
.opensymphony.sitemesh.webapp.SiteMeshFilter.doFilter(SiteMeshFilter.java:65)
 at org
.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
 at org
.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:217)
 at org
.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:279)
 at org
.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
 at org
.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)
 at org
.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)
 at org
.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)
 at org
.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:331)
 at org
.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)
 at com
.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)
 at com
.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)
 at com
.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)
 at com
.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)
 at com
.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)
 at com
.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)
 at com
.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)
 at com
.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)
 at com
.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)
 at com
.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)
 at com
.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)
 at com
.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)
 at com
.sun.grizzly.ContextTask.run(ContextTask.java:71)
 at com
.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)
 at com
.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)
 at java
.lang.Thread.run(Thread.java:722)
2014-01-10 17:25:12.113+0000: TM error tx commit Unable to rollback ---> error in commit: java.nio.BufferOverflowException ---> error code for rollback: Uknown error code
javax
.transaction.HeuristicMixedException: Unable to rollback ---> error in commit: java.nio.BufferOverflowException ---> error code for rollback: Uknown error code
 at org
.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:492)
 at org
.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:406)
 at org
.neo4j.kernel.impl.transaction.TransactionImpl.commit(TransactionImpl.java:117)
 at org
.neo4j.kernel.TopLevelTransaction.finish(TopLevelTransaction.java:115)
 at javax
.servlet.http.HttpServlet.service(HttpServlet.java:688)
 at javax
.servlet.http.HttpServlet.service(HttpServlet.java:770)
 at org
.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)
 at org
.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:343)
 at org
.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:217)
 at com
.opensymphony.sitemesh.webapp.SiteMeshFilter.doFilter(SiteMeshFilter.java:65)
 at org
.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
 at org
.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:217)
 at org
.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:279)
 at org
.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
 at org
.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)
 at org
.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)
 at org
.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)
 at org
.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:331)
 at org
.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)
 at com
.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)
 at com
.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)
 at com
.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)
 at com
.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)
 at com
.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)
 at com
.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)
 at com
.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)
 at com
.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)
 at com
.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)
 at com
.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)
 at com
.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)
 at com
.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)
 at com
.sun.grizzly.ContextTask.run(ContextTask.java:71)
 at com
.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)
 at com
.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)
 at java
.lang.Thread.run(Thread.java:722)
Caused by: java.nio.BufferOverflowException
 at java
.nio.Buffer.nextPutIndex(Buffer.java:513)
 at java
.nio.DirectByteBuffer.put(DirectByteBuffer.java:291)
 at org
.neo4j.kernel.impl.transaction.xaframework.DirectMappedLogBuffer.put(DirectMappedLogBuffer.java:65)
 at org
.neo4j.kernel.impl.transaction.xaframework.LogIoUtils.writeStart(LogIoUtils.java:246)
 at org
.neo4j.kernel.impl.transaction.xaframework.XaLogicalLog.writeStartEntry(XaLogicalLog.java:303)
 at org
.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.checkStartWritten(XaResourceManager.java:307)
 at org
.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.rollback(XaResourceManager.java:512)
 at org
.neo4j.kernel.impl.transaction.xaframework.XaResourceHelpImpl.rollback(XaResourceHelpImpl.java:111)
 at org
.neo4j.kernel.impl.transaction.TransactionImpl.doRollback(TransactionImpl.java:558)
 at org
.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:469)
 
... 38 more
2014-01-10 18:16:07.769+0000: GC Monitor: Application threads blocked for an additional 583ms [total block time: 510.108s]
2014-01-10 19:16:08.361+0000: GC Monitor: Application threads blocked for an additional 533ms [total block time: 510.641s]
2014-01-10 20:16:09.018+0000: GC Monitor: Application threads blocked for an additional 565ms [total block time: 511.206s]
2014-01-10 21:16:09.696+0000: GC Monitor: Application threads blocked for an additional 616ms [total block time: 511.822s]
2014-01-10 22:16:10.286+0000: GC Monitor: Application threads blocked for an additional 506ms [total block time: 512.328s]
2014-01-10 23:16:10.873+0000: GC Monitor: Application threads blocked for an additional 495ms [total block time: 512.823s]
2014-01-11 00:16:11.444+0000: GC Monitor: Application threads blocked for an additional 489ms [total block time: 513.312s]
2014-01-11 01:16:12.052+0000:  
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