I'm loading a large number of nodes and relationships into an embedded Neo4j database. After about 10,000 inserts, it dies. If I stay under that point, then everything works great. Queries return as they should, as do inserts. It looks like somehow a database file is getting deleted in the middle of the inserts, which is causing everything to fall apart. My database builds itself from scratch, so if I completely delete my graphdb folder and restart it, it runs exactly the same every time. So how do you handle large embedded Neo4j databases?
Here are the pertinent errors.
From the Java output side
The transactions start not committing:
WorkerThread exception::org.neo4j.graphdb.TransactionFailureException::Unable to commit transaction
org.neo4j.graphdb.TransactionFailureException: Unable to commit transaction
at org.neo4j.kernel.TopLevelTransaction.close(TopLevelTransaction.java:140)
...
at java.lang.Thread.run(Thread.java:745)
Caused by: org.neo4j.graphdb.TransactionFailureException: commit threw exception
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:500)
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:385)
at org.neo4j.kernel.impl.transaction.TransactionImpl.commit(TransactionImpl.java:123)
at org.neo4j.kernel.TopLevelTransaction.close(TopLevelTransaction.java:124)
... 4 more
Caused by: javax.transaction.xa.XAException
Then it informs me that there's a missing file in the database:
saction.TransactionImpl.doCommit(TransactionImpl.java:560)
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:448)
... 7 more
Caused by: org.neo4j.kernel.impl.nioneo.store.UnderlyingStorageException: java.io.FileNotFoundException: /home/user/graphdb/schema/label/lucene/_1z6.frq (Protocol error)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransaction.updateLabelScanStore(NeoStoreTransaction.java:814)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransaction.applyCommit(NeoStoreTransaction.java:699)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransaction.doCommit(NeoStoreTransaction.java:631)
at org.neo4j.kernel.impl.transaction.xaframework.XaTransaction.commit(XaTransaction.java:327)
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.commitWriteTx(XaResourceManager.java:632)
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.commit(XaResourceManager.java:533)
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceHelpImpl.commit(XaResourceHelpImpl.java:64)
at org.neo4j.kernel.impl.transaction.TransactionImpl.doCommit(TransactionImpl.java:548)
... 8 more
Caused by: java.io.FileNotFoundException: /home/user/graphdb/schema/label/lucene/_1z6.frq (Protocol error)
at java.io.RandomAccessFile.open(Native Method)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:241)
at org.apache.lucene.store.FSDirectory$FSIndexOutput.<init>(FSDirectory.java:441)
at org.apache.lucene.store.FSDirectory.createOutput(FSDirectory.java:306)
at org.apache.lucene.index.FormatPostingsDocsWriter.<init>(FormatPostingsDocsWriter.java:47)
at org.apache.lucene.index.FormatPostingsTermsWriter.<init>(FormatPostingsTermsWriter.java:33)
at org.apache.lucene.index.FormatPostingsFieldsWriter.<init>(FormatPostingsFieldsWriter.java:51)
at org.apache.lucene.index.FreqProxTermsWriter.flush(FreqProxTermsWriter.java:85)
at org.apache.lucene.index.TermsHash.flush(TermsHash.java:113)
at org.apache.lucene.index.DocInverter.flush(DocInverter.java:70)
at org.apache.lucene.index.DocFieldProcessor.flush(DocFieldProcessor.java:60)
at org.apache.lucene.index.DocumentsWriter.flush(DocumentsWriter.java:581)
at org.apache.lucene.index.IndexWriter.doFlush(IndexWriter.java:3587)
at org.apache.lucene.index.IndexWriter.flush(IndexWriter.java:3552)
at org.apache.lucene.index.IndexWriter.getReader(IndexWriter.java:450)
at org.apache.lucene.index.IndexWriter.getReader(IndexWriter.java:399)
at org.apache.lucene.index.DirectoryReader.doOpenFromWriter(DirectoryReader.java:413)
at org.apache.lucene.index.DirectoryReader.doOpenIfChanged(DirectoryReader.java:432)
at org.apache.lucene.index.DirectoryReader.doOpenIfChanged(DirectoryReader.java:375)
at org.apache.lucene.index.IndexReader.openIfChanged(IndexReader.java:508)
at org.apache.lucene.search.SearcherManager.refreshIfNeeded(SearcherManager.java:109)
at org.apache.lucene.search.SearcherManager.refreshIfNeeded(SearcherManager.java:57)
at org.apache.lucene.search.ReferenceManager.maybeRefresh(ReferenceManager.java:137)
at org.neo4j.kernel.api.impl.index.LuceneLabelScanStore.refreshSearcher(LuceneLabelScanStore.java:159)
at org.neo4j.kernel.api.impl.index.LuceneLabelScanWriter.close(LuceneLabelScanWriter.java:82)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransaction.updateLabelScanStore(NeoStoreTransaction.java:811)
... 15 more
Then I can no longer get a new transaction:
WorkerThread exception::org.neo4j.graphdb.TransactionFailureException::Unable to get transaction.
org.neo4j.graphdb.TransactionFailureException: Unable to get transaction.
at org.neo4j.kernel.InternalAbstractGraphDatabase.transactionRunning(InternalAbstractGraphDatabase.java:1064)
at org.neo4j.kernel.InternalAbstractGraphDatabase.beginTx(InternalAbstractGraphDatabase.java:1037)
at org.neo4j.kernel.TransactionBuilderImpl.begin(TransactionBuilderImpl.java:43)
at org.neo4j.kernel.InternalAbstractGraphDatabase.beginTx(InternalAbstractGraphDatabase.java:1024)
...
at java.lang.Thread.run(Thread.java:745)
Caused by: javax.transaction.SystemException: Kernel has encountered some problem, please perform neccesary action (tx recovery/restart)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.neo4j.kernel.impl.transaction.KernelHealth.assertHealthy(KernelHealth.java:61)
at org.neo4j.kernel.impl.transaction.TxManager.assertTmOk(TxManager.java:339)
at org.neo4j.kernel.impl.transaction.TxManager.getTransaction(TxManager.java:725)
at org.neo4j.kernel.InternalAbstractGraphDatabase.transactionRunning(InternalAbstractGraphDatabase.java:1060)
... 7 more
Caused by: javax.transaction.xa.XAException
at org.neo4j.kernel.impl.transaction.TransactionImpl.doCommit(TransactionImpl.java:560)
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:448)
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:385)
at org.neo4j.kernel.impl.transaction.TransactionImpl.commit(TransactionImpl.java:123)
at org.neo4j.kernel.TopLevelTransaction.close(TopLevelTransaction.java:124)
... 4 more
Caused by: org.neo4j.kernel.impl.nioneo.store.UnderlyingStorageException: java.io.FileNotFoundException: /home/user/graphdb/schema/label/lucene/_1z6.frq (Protocol error)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransaction.updateLabelScanStore(NeoStoreTransaction.java:814)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransaction.applyCommit(NeoStoreTransaction.java:699)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransaction.doCommit(NeoStoreTransaction.java:631)
at org.neo4j.kernel.impl.transaction.xaframework.XaTransaction.commit(XaTransaction.java:327)
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.commitWriteTx(XaResourceManager.java:632)
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.commit(XaResourceManager.java:533)
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceHelpImpl.commit(XaResourceHelpImpl.java:64)
at org.neo4j.kernel.impl.transaction.TransactionImpl.doCommit(TransactionImpl.java:548)
... 8 more
Caused by: java.io.FileNotFoundException: /home/user/graphdb/schema/label/lucene/_1z6.frq (Protocol error)
at java.io.RandomAccessFile.open(Native Method)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:241)
at org.apache.lucene.store.FSDirectory$FSIndexOutput.<init>(FSDirectory.java:441)
at org.apache.lucene.store.FSDirectory.createOutput(FSDirectory.java:306)
at org.apache.lucene.index.FormatPostingsDocsWriter.<init>(FormatPostingsDocsWriter.java:47)
at org.apache.lucene.index.FormatPostingsTermsWriter.<init>(FormatPostingsTermsWriter.java:33)
at org.apache.lucene.index.FormatPostingsFieldsWriter.<init>(FormatPostingsFieldsWriter.java:51)
at org.apache.lucene.index.FreqProxTermsWriter.flush(FreqProxTermsWriter.java:85)
at org.apache.lucene.index.TermsHash.flush(TermsHash.java:113)
at org.apache.lucene.index.DocInverter.flush(DocInverter.java:70)
at org.apache.lucene.index.DocFieldProcessor.flush(DocFieldProcessor.java:60)
at org.apache.lucene.index.DocumentsWriter.flush(DocumentsWriter.java:581)
at org.apache.lucene.index.IndexWriter.doFlush(IndexWriter.java:3587)
at org.apache.lucene.index.IndexWriter.flush(IndexWriter.java:3552)
at org.apache.lucene.index.IndexWriter.getReader(IndexWriter.java:450)
at org.apache.lucene.index.IndexWriter.getReader(IndexWriter.java:399)
at org.apache.lucene.index.DirectoryReader.doOpenFromWriter(DirectoryReader.java:413)
at org.apache.lucene.index.DirectoryReader.doOpenIfChanged(DirectoryReader.java:432)
at org.apache.lucene.index.DirectoryReader.doOpenIfChanged(DirectoryReader.java:375)
at org.apache.lucene.index.IndexReader.openIfChanged(IndexReader.java:508)
at org.apache.lucene.search.SearcherManager.refreshIfNeeded(SearcherManager.java:109)
at org.apache.lucene.search.SearcherManager.refreshIfNeeded(SearcherManager.java:57)
at org.apache.lucene.search.ReferenceManager.maybeRefresh(ReferenceManager.java:137)
at org.neo4j.kernel.api.impl.index.LuceneLabelScanStore.refreshSearcher(LuceneLabelScanStore.java:159)
at org.neo4j.kernel.api.impl.index.LuceneLabelScanWriter.close(LuceneLabelScanWriter.java:82)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransaction.updateLabelScanStore(NeoStoreTransaction.java:811)
... 15 more
From the messages.log side
It starts off getting memory mapping errors. This actually happens first when the database first comes online. But more trickle in before it totally dies:
2015-01-27 21:51:29.112+0000 ERROR [org.neo4j]: [/home/user/graphdb/neostore.nodestore.db] Unable to memory map Unable to map pos=0 recordSize=15 totalSize=1048575
org.neo4j.kernel.impl.nioneo.store.MappedMemException: Unable to map pos=0 recordSize=15 totalSize=1048575
at org.neo4j.kernel.impl.nioneo.store.MappedPersistenceWindow.<init>(MappedPersistenceWindow.java:59)
at org.neo4j.kernel.impl.nioneo.store.PersistenceWindowPool.allocateNewWindow(PersistenceWindowPool.java:656)
at org.neo4j.kernel.impl.nioneo.store.PersistenceWindowPool.expandBricks(PersistenceWindowPool.java:617)
at org.neo4j.kernel.impl.nioneo.store.PersistenceWindowPool.acquire(PersistenceWindowPool.java:144)
at org.neo4j.kernel.impl.nioneo.store.CommonAbstractStore.acquireWindow(CommonAbstractStore.java:546)
at org.neo4j.kernel.impl.nioneo.store.NodeStore.forceGetRecord(NodeStore.java:149)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreIndexStoreView$NodeStoreScan.run(NeoStoreIndexStoreView.java:327)
at org.neo4j.kernel.impl.api.index.IndexPopulationJob.indexAllNodes(IndexPopulationJob.java:212)
at org.neo4j.kernel.impl.api.index.IndexPopulationJob.run(IndexPopulationJob.java:107)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: Invalid argument
at sun.nio.ch.FileChannelImpl.map0(Native Method)
at sun.nio.ch.FileChannelImpl.map(FileChannelImpl.java:875)
at org.neo4j.kernel.impl.nioneo.store.StoreFileChannel.map(StoreFileChannel.java:57)
at org.neo4j.kernel.impl.nioneo.store.MappedPersistenceWindow.<init>(MappedPersistenceWindow.java:53)
... 13 more
Then, and I've figured out that this is when everything falls apart, I get this error in messages.log:
2015-01-27 21:59:41.516+0000 ERROR [org.neo4j]: setting TM not OK. Kernel has encountered some problem, please perform neccesary action (tx recovery/restart) null
javax.transaction.xa.XAException
at org.neo4j.kernel.impl.transaction.TransactionImpl.doCommit(TransactionImpl.java:560)
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:448)
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:385)
at org.neo4j.kernel.impl.transaction.TransactionImpl.commit(TransactionImpl.java:123)
at org.neo4j.kernel.TopLevelTransaction.close(TopLevelTransaction.java:124)
...
at java.lang.Thread.run(Thread.java:745)
Caused by: org.neo4j.kernel.impl.nioneo.store.UnderlyingStorageException: java.io.FileNotFoundException: /home/user/graphdb/schema/label/lucene/_1z6.frq (Protocol error)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransaction.updateLabelScanStore(NeoStoreTransaction.java:814)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransaction.applyCommit(NeoStoreTransaction.java:699)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransaction.doCommit(NeoStoreTransaction.java:631)
at org.neo4j.kernel.impl.transaction.xaframework.XaTransaction.commit(XaTransaction.java:327)
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.commitWriteTx(XaResourceManager.java:632)
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.commit(XaResourceManager.java:533)
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceHelpImpl.commit(XaResourceHelpImpl.java:64)
at org.neo4j.kernel.impl.transaction.TransactionImpl.doCommit(TransactionImpl.java:548)
... 8 more
Caused by: java.io.FileNotFoundException: /home/user/graphdb/schema/label/lucene/_1z6.frq (Protocol error)
at java.io.RandomAccessFile.open(Native Method)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:241)
at org.apache.lucene.store.FSDirectory$FSIndexOutput.<init>(FSDirectory.java:441)
at org.apache.lucene.store.FSDirectory.createOutput(FSDirectory.java:306)
at org.apache.lucene.index.FormatPostingsDocsWriter.<init>(FormatPostingsDocsWriter.java:47)
at org.apache.lucene.index.FormatPostingsTermsWriter.<init>(FormatPostingsTermsWriter.java:33)
at org.apache.lucene.index.FormatPostingsFieldsWriter.<init>(FormatPostingsFieldsWriter.java:51)
at org.apache.lucene.index.FreqProxTermsWriter.flush(FreqProxTermsWriter.java:85)
at org.apache.lucene.index.TermsHash.flush(TermsHash.java:113)
at org.apache.lucene.index.DocInverter.flush(DocInverter.java:70)
at org.apache.lucene.index.DocFieldProcessor.flush(DocFieldProcessor.java:60)
at org.apache.lucene.index.DocumentsWriter.flush(DocumentsWriter.java:581)
at org.apache.lucene.index.IndexWriter.doFlush(IndexWriter.java:3587)
at org.apache.lucene.index.IndexWriter.flush(IndexWriter.java:3552)
at org.apache.lucene.index.IndexWriter.getReader(IndexWriter.java:450)
at org.apache.lucene.index.IndexWriter.getReader(IndexWriter.java:399)
at org.apache.lucene.index.DirectoryReader.doOpenFromWriter(DirectoryReader.java:413)
at org.apache.lucene.index.DirectoryReader.doOpenIfChanged(DirectoryReader.java:432)
at org.apache.lucene.index.DirectoryReader.doOpenIfChanged(DirectoryReader.java:375)
at org.apache.lucene.index.IndexReader.openIfChanged(IndexReader.java:508)
at org.apache.lucene.search.SearcherManager.refreshIfNeeded(SearcherManager.java:109)
at org.apache.lucene.search.SearcherManager.refreshIfNeeded(SearcherManager.java:57)
at org.apache.lucene.search.ReferenceManager.maybeRefresh(ReferenceManager.java:137)
at org.neo4j.kernel.api.impl.index.LuceneLabelScanStore.refreshSearcher(LuceneLabelScanStore.java:159)
at org.neo4j.kernel.api.impl.index.LuceneLabelScanWriter.close(LuceneLabelScanWriter.java:82)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransaction.updateLabelScanStore(NeoStoreTransaction.java:811)
... 15 more
2015-01-27 21:59:41.519+0000 ERROR [org.neo4j]: TM error tx commit commit threw exception
Any ideas on what's causing that .frq file to disappear?
We resolved it in a side-conversation, maximum open files was too low (4000) which is also reported at startup.
That causes Lucene to break internally.
After increasing the limit the OP could import the data successfully.
Related
I installed a new subversion repository but I am unable to connect to the repository.
In the old repository it is working as expected. The new repository thorws an exception:
org.eclipse.team.svn.core.connector.SVNConnectorException: svn: E210002: There was a problem while connecting to xn--x7h.example.com:22
at org.polarion.team.svn.connector.svnkit.SVNKitService.handleClientException(SVNKitService.java:59)
at org.polarion.team.svn.connector.svnkit.SVNKitConnector.listEntries(SVNKitConnector.java:1758)
at org.eclipse.team.svn.core.extension.factory.ThreadNameModifier.listEntries(ThreadNameModifier.java:324)
at org.eclipse.team.svn.core.utility.SVNUtility.list(SVNUtility.java:440)
at org.eclipse.team.svn.core.svnstorage.SVNRepositoryContainer.getChildren(SVNRepositoryContainer.java:79)
at org.eclipse.team.svn.core.operation.remote.GetRemoteFolderChildrenOperation.runImpl(GetRemoteFolderChildrenOperation.java:76)
at org.eclipse.team.svn.core.operation.AbstractActionOperation.run(AbstractActionOperation.java:82)
at org.eclipse.team.svn.core.utility.ProgressMonitorUtility.doTask(ProgressMonitorUtility.java:104)
at org.eclipse.team.svn.core.operation.CompositeOperation.runImpl(CompositeOperation.java:99)
at org.eclipse.team.svn.core.operation.AbstractActionOperation.run(AbstractActionOperation.java:82)
at org.eclipse.team.svn.core.operation.LoggedOperation.run(LoggedOperation.java:40)
at org.eclipse.team.svn.core.utility.ProgressMonitorUtility.doTask(ProgressMonitorUtility.java:104)
at org.eclipse.team.svn.core.utility.ProgressMonitorUtility.doTaskExternal(ProgressMonitorUtility.java:90)
at org.eclipse.team.svn.ui.utility.DefaultCancellableOperationWrapper.run(DefaultCancellableOperationWrapper.java:55)
at org.eclipse.team.svn.ui.utility.ScheduledOperationWrapper.run(ScheduledOperationWrapper.java:37)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:63)
Caused by: org.apache.subversion.javahl.ClientException: svn: E210002: There was a problem while connecting to xn--x7h.example.com:22
at org.apache.subversion.javahl.ClientException.fromException(ClientException.java:117)
at org.tmatesoft.svn.core.javahl17.SVNClientImpl.getClientException(SVNClientImpl.java:1539)
at org.tmatesoft.svn.core.javahl17.SVNClientImpl.list(SVNClientImpl.java:189)
at org.polarion.team.svn.connector.svnkit.SVNKitConnector.listEntries(SVNKitConnector.java:1745)
... 14 more
Caused by: org.tmatesoft.svn.core.SVNException: svn: E210002: There was a problem while connecting to xn--x7h.example.com:22
at org.tmatesoft.svn.core.internal.wc.SVNErrorManager.error(SVNErrorManager.java:70)
at org.tmatesoft.svn.core.internal.wc.SVNErrorManager.error(SVNErrorManager.java:57)
at org.tmatesoft.svn.core.internal.io.svn.SVNSSHConnector.open(SVNSSHConnector.java:145)
at org.tmatesoft.svn.core.internal.io.svn.SVNConnection.open(SVNConnection.java:77)
at org.tmatesoft.svn.core.internal.io.svn.SVNRepositoryImpl.openConnection(SVNRepositoryImpl.java:1273)
at org.tmatesoft.svn.core.internal.io.svn.SVNRepositoryImpl.getLatestRevision(SVNRepositoryImpl.java:172)
at org.tmatesoft.svn.core.internal.wc2.ng.SvnNgRepositoryAccess.getRevisionNumber(SvnNgRepositoryAccess.java:119)
at org.tmatesoft.svn.core.internal.wc2.SvnRepositoryAccess.getLocations(SvnRepositoryAccess.java:195)
at org.tmatesoft.svn.core.internal.wc2.ng.SvnNgRepositoryAccess.createRepositoryFor(SvnNgRepositoryAccess.java:46)
at org.tmatesoft.svn.core.internal.wc2.remote.SvnRemoteList.run(SvnRemoteList.java:36)
at org.tmatesoft.svn.core.internal.wc2.remote.SvnRemoteList.run(SvnRemoteList.java:1)
at org.tmatesoft.svn.core.internal.wc2.SvnOperationRunner.run(SvnOperationRunner.java:21)
at org.tmatesoft.svn.core.wc2.SvnOperationFactory.run(SvnOperationFactory.java:1235)
at org.tmatesoft.svn.core.wc2.SvnOperation.run(SvnOperation.java:294)
at org.tmatesoft.svn.core.javahl17.SVNClientImpl.list(SVNClientImpl.java:187)
... 15 more
Caused by: java.io.IOException: There was a problem while connecting to xn--x7h.example.com:22
at com.trilead.ssh2.Connection.connect(Connection.java:817)
at org.tmatesoft.svn.core.internal.io.svn.ssh.SshHost.openConnection(SshHost.java:225)
at org.tmatesoft.svn.core.internal.io.svn.ssh.SshHost.openSession(SshHost.java:153)
at org.tmatesoft.svn.core.internal.io.svn.ssh.SshSessionPool.openSession(SshSessionPool.java:85)
at org.tmatesoft.svn.core.internal.io.svn.SVNSSHConnector.open(SVNSSHConnector.java:122)
... 27 more
Caused by: java.io.IOException: Key exchange was not finished, connection is closed.
at com.trilead.ssh2.transport.KexManager.getOrWaitForConnectionInfo(KexManager.java:92)
at com.trilead.ssh2.transport.TransportManager.getConnectionInfo(TransportManager.java:231)
at com.trilead.ssh2.Connection.connect(Connection.java:769)
... 31 more
Caused by: java.io.IOException: Cannot negotiate, proposals do not match.
at com.trilead.ssh2.transport.KexManager.handleMessage(KexManager.java:413)
at com.trilead.ssh2.transport.TransportManager.receiveLoop(TransportManager.java:765)
at com.trilead.ssh2.transport.TransportManager$1.run(TransportManager.java:480)
at java.base/java.lang.Thread.run(Thread.java:834)
Any ideas?
I checked on server-side what is going on. So I called tail -f /var/log/auth.log and discovered a message that the client and the server was not able to agree on matching kex-algorithms.
Finally my solution was to enable the line
KexAlgorithms +diffie-hellman-group1-sha1
to the corresponding
/etc/ssh/sshd_config
File and restart the sshd-server.
I know this kind of question have been asked previously, but I still don't get solution after reading their posts, so I decide to post this question again from here.
I Am working on Java multi-threaded application where I am trying to run HQL queries using JDBC on Hive environment. I have bunch of hive-sql queries and i am executing them on Hive in parallel with multiple threads and I am getting following exception when queries count more (for example, if i am running more than 100 queries). can some one please check this and help me on this?
2020-06-16 06:00:45,314 ERROR [main]: Terminal exception
java.lang.Exception: Map step agg_cas_auth_reinstate_derive failed.
at com.mine.idn.magellan.ParallelExecGraph.execute(ParallelExecGraph.java:198)
at com.mine.idn.magellan.WarehouseSession.executeMap(WarehouseSession.java:332)
at com.mine.idn.magellan.StandAloneEnv.execute(StandAloneEnv.java:872)
at com.mine.idn.magellan.StandAloneEnv.execute(StandAloneEnv.java:778)
at com.mine.idn.magellan.StandAloneEnv.executeAndExit(StandAloneEnv.java:642)
at com.mine.idn.magellan.StandAloneEnv.main(StandAloneEnv.java:77)
Caused by: java.sql.SQLException: org.apache.hive.service.cli.HiveSQLException: Error while processing statement: FAILED: Execution Error, return code 1 from org.apache.hadoop.hive.ql.exec.mr.MapRedTask. java.io.IOException: Bad file descriptor
at org.apache.hive.service.cli.operation.Operation.toSQLException(Operation.java:380)
at org.apache.hive.service.cli.operation.SQLOperation.runQuery(SQLOperation.java:257)
at org.apache.hive.service.cli.operation.SQLOperation.access$800(SQLOperation.java:91)
at org.apache.hive.service.cli.operation.SQLOperation$BackgroundWork$1.run(SQLOperation.java:348)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1669)
at org.apache.hive.service.cli.operation.SQLOperation$BackgroundWork.run(SQLOperation.java:362)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: java.io.IOException: Bad file descriptor
at org.apache.hadoop.conf.Configuration.loadResource(Configuration.java:2850)
at org.apache.hadoop.conf.Configuration.loadResources(Configuration.java:2685)
at org.apache.hadoop.conf.Configuration.getProps(Configuration.java:2591)
at org.apache.hadoop.conf.Configuration.get(Configuration.java:1077)
at org.apache.hadoop.mapred.JobConf.checkAndWarnDeprecation(JobConf.java:2007)
at org.apache.hadoop.mapred.JobConf.<init>(JobConf.java:479)
at org.apache.hadoop.mapred.JobConf.<init>(JobConf.java:469)
at org.apache.hadoop.mapreduce.Cluster.getJob(Cluster.java:190)
at org.apache.hadoop.mapred.JobClient$2.run(JobClient.java:601)
at org.apache.hadoop.mapred.JobClient$2.run(JobClient.java:599)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1669)
at org.apache.hadoop.mapred.JobClient.getJobUsingCluster(JobClient.java:599)
at org.apache.hadoop.mapred.JobClient.getJobInner(JobClient.java:609)
at org.apache.hadoop.mapred.JobClient.getJob(JobClient.java:639)
at org.apache.hadoop.hive.ql.exec.mr.HadoopJobExecHelper.progress(HadoopJobExecHelper.java:295)
at org.apache.hadoop.hive.ql.exec.mr.HadoopJobExecHelper.progress(HadoopJobExecHelper.java:559)
at org.apache.hadoop.hive.ql.exec.mr.ExecDriver.execute(ExecDriver.java:425)
at org.apache.hadoop.hive.ql.exec.mr.MapRedTask.execute(MapRedTask.java:151)
at org.apache.hadoop.hive.ql.exec.Task.executeTask(Task.java:201)
at org.apache.hadoop.hive.ql.exec.TaskRunner.runSequential(TaskRunner.java:100)
at org.apache.hadoop.hive.ql.exec.TaskRunner.run(TaskRunner.java:79)
Caused by: java.io.IOException: Bad file descriptor
at java.io.FileInputStream.close0(Native Method)
at java.io.FileInputStream.access$000(FileInputStream.java:49)
at java.io.FileInputStream$1.close(FileInputStream.java:336)
at java.io.FileDescriptor.closeAll(FileDescriptor.java:212)
at java.io.FileInputStream.close(FileInputStream.java:334)
at java.io.BufferedInputStream.close(BufferedInputStream.java:483)
at org.apache.hadoop.conf.Configuration.parse(Configuration.java:2676)
at org.apache.hadoop.conf.Configuration.parse(Configuration.java:2661)
at org.apache.hadoop.conf.Configuration.loadResource(Configuration.java:2741)
... 22 more
at org.apache.hive.jdbc.HiveStatement.waitForOperationToComplete(HiveStatement.java:385)
at org.apache.hive.jdbc.HiveStatement.execute(HiveStatement.java:254)
at com.mine.idn.magellan.WarehouseSession.executeMapStep(WarehouseSession.java:797)
at com.mine.idn.magellan.WarehouseSession.access$000(WarehouseSession.java:23)
at com.mine.idn.magellan.WarehouseSession$ParallelExecResources.executeMapStep(WarehouseSession.java:91)
at com.mine.idn.magellan.ParallelExecGraph$Node.run(ParallelExecGraph.java:85)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
What i dont understand is, why hadoop framework throwing - Bad File Descriptor Exception? My Java code invoking Hadoop-Hive code and its throwing this exception.
Also one more thing is this issue is intermittent, not consistent. If i re-run the same application, most of the cases, it went through.
Thank you for
I wrote a mapreduce job to scan an hbase table for a certain time range to count certain elements we need for analysis.
Mappers in the MR job keeps failing but I don't know why. Seems like each time I run the job, a different number of mappers fail. The YARN log (see below) from Cloudera manager isn't helpful in pointing what the problem is, although, someone said I might be running out of memory.
It seems to retry multiple times but each time it fails. What do I need to do to make it stop failing or how can I log things to help me better determine what is happening?
Below is a log from YARN for one of the mappers that failed.
Error: org.apache.hadoop.hbase.client.RetriesExhaustedException:
Failed after attempts=36, exceptions: Thu Jun 15 16:26:57 PDT 2017,
null, java.net.SocketTimeoutException: callTimeout=60000,
callDuration=60301: row '152_p3401.db161139.sjc102.dbi_1496271480' on
table 'dbi_based_data' at
region=dbi_based_data,151_p3413.db162024.iad4.dbi_1476974340,1486675565213.d83250d0682e648d165872afe5abd60e., hostname=hslave35118.ams9.mysecretdomain.com,60020,1483570489305,
seqNum=19308931 at
org.apache.hadoop.hbase.client.RpcRetryingCallerWithReadReplicas.throwEnrichedException(RpcRetryingCallerWithReadReplicas.java:276)
at
org.apache.hadoop.hbase.client.ScannerCallableWithReplicas.call(ScannerCallableWithReplicas.java:207)
at
org.apache.hadoop.hbase.client.ScannerCallableWithReplicas.call(ScannerCallableWithReplicas.java:60)
at
org.apache.hadoop.hbase.client.RpcRetryingCaller.callWithoutRetries(RpcRetryingCaller.java:200)
at
org.apache.hadoop.hbase.client.ClientScanner.call(ClientScanner.java:320)
at
org.apache.hadoop.hbase.client.ClientScanner.loadCache(ClientScanner.java:403)
at
org.apache.hadoop.hbase.client.ClientScanner.next(ClientScanner.java:364)
at
org.apache.hadoop.hbase.mapreduce.TableRecordReaderImpl.nextKeyValue(TableRecordReaderImpl.java:236)
at
org.apache.hadoop.hbase.mapreduce.TableRecordReader.nextKeyValue(TableRecordReader.java:147)
at
org.apache.hadoop.hbase.mapreduce.TableInputFormatBase$1.nextKeyValue(TableInputFormatBase.java:216)
at
org.apache.hadoop.mapred.MapTask$NewTrackingRecordReader.nextKeyValue(MapTask.java:556)
at
org.apache.hadoop.mapreduce.task.MapContextImpl.nextKeyValue(MapContextImpl.java:80)
at
org.apache.hadoop.mapreduce.lib.map.WrappedMapper$Context.nextKeyValue(WrappedMapper.java:91)
at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:144) at
org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:787) at
org.apache.hadoop.mapred.MapTask.run(MapTask.java:341) at
org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:164) at
java.security.AccessController.doPrivileged(Native Method) at
javax.security.auth.Subject.doAs(Subject.java:415) at
org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1693)
at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158) Caused
by: java.net.SocketTimeoutException: callTimeout=60000,
callDuration=60301: row '152_p3401.db161139.sjc102.dbi_1496271480' on
table 'dbi_based_data' at
region=dbi_based_data,151_p3413.db162024.iad4.dbi_1476974340,1486675565213.d83250d0682e648d165872afe5abd60e., hostname=hslave35118.ams9.mysecretdomain.com,60020,1483570489305,
seqNum=19308931 at
org.apache.hadoop.hbase.client.RpcRetryingCaller.callWithRetries(RpcRetryingCaller.java:159)
at
org.apache.hadoop.hbase.client.ResultBoundedCompletionService$QueueingFuture.run(ResultBoundedCompletionService.java:65)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745) Caused by:
java.io.IOException: Call to
hslave35118.ams9.mysecretdomain.com/10.216.35.118:60020 failed on
local exception: org.apache.hadoop.hbase.ipc.CallTimeoutException:
Call id=12, waitTime=60001, operationTimeout=60000 expired. at
org.apache.hadoop.hbase.ipc.AbstractRpcClient.wrapException(AbstractRpcClient.java:291)
at
org.apache.hadoop.hbase.ipc.RpcClientImpl.call(RpcClientImpl.java:1272)
at
org.apache.hadoop.hbase.ipc.AbstractRpcClient.callBlockingMethod(AbstractRpcClient.java:226)
at
org.apache.hadoop.hbase.ipc.AbstractRpcClient$BlockingRpcChannelImplementation.callBlockingMethod(AbstractRpcClient.java:331)
at
org.apache.hadoop.hbase.protobuf.generated.ClientProtos$ClientService$BlockingStub.scan(ClientProtos.java:34094)
at
org.apache.hadoop.hbase.client.ScannerCallable.call(ScannerCallable.java:219)
at
org.apache.hadoop.hbase.client.ScannerCallable.call(ScannerCallable.java:64)
at
org.apache.hadoop.hbase.client.RpcRetryingCaller.callWithoutRetries(RpcRetryingCaller.java:200)
at
org.apache.hadoop.hbase.client.ScannerCallableWithReplicas$RetryingRPC.call(ScannerCallableWithReplicas.java:360)
at
org.apache.hadoop.hbase.client.ScannerCallableWithReplicas$RetryingRPC.call(ScannerCallableWithReplicas.java:334)
at
org.apache.hadoop.hbase.client.RpcRetryingCaller.callWithRetries(RpcRetryingCaller.java:126)
... 4 more Caused by:
org.apache.hadoop.hbase.ipc.CallTimeoutException: Call id=12,
waitTime=60001, operationTimeout=60000 expired. at
org.apache.hadoop.hbase.ipc.Call.checkAndSetTimeout(Call.java:73) at
org.apache.hadoop.hbase.ipc.RpcClientImpl.call(RpcClientImpl.java:1246)
... 13 more
So it looks like for my case I needed to extend the timeout setting. In my Java program I had to add the following lines to make the exception go away:
conf.set("hbase.rpc.timeout","90000");
conf.set("hbase.client.scanner.timeout.period","90000");
The answer was found on this link on Cloudera's site
I am using embedded version of H2 1.4.191 with the following connection string:
jdbc:h2:<Path of database file>
I am facing two problems:
Sometimes my database size goes beyond 10GB and system stops working. I think the data stored in db should not take more than 5Mb. What is consuming memory?
Sometimes I am getting these exception :
org.h2.jdbc.JdbcSQLException: File corrupted while reading record: null. Possible solution: use the recovery tool [90030-191]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:345)
at org.h2.message.DbException.get(DbException.java:168)
at org.h2.mvstore.db.MVTableEngine$Store.convertIllegalStateException(MVTableEngine.java:195)
at org.h2.mvstore.db.MVTableEngine$Store.open(MVTableEngine.java:167)
at org.h2.mvstore.db.MVTableEngine.init(MVTableEngine.java:99)
at org.h2.engine.Database.getPageStore(Database.java:2460)
at org.h2.engine.Database.open(Database.java:692)
at org.h2.engine.Database.openDatabase(Database.java:270)
at org.h2.engine.Database.(Database.java:264)
at org.h2.engine.Engine.openSession(Engine.java:65)
at org.h2.engine.Engine.openSession(Engine.java:175)
at org.h2.engine.Engine.createSessionAndValidate(Engine.java:153)
at org.h2.engine.Engine.createSession(Engine.java:136)
at org.h2.engine.Engine.createSession(Engine.java:28)
at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:349)
at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:107)
at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:91)
at org.h2.Driver.connect(Driver.java:72)
at java.sql.DriverManager.getConnection(Unknown Source)
at java.sql.DriverManager.getConnection(Unknown Source)
at com.j256.ormlite.jdbc.JdbcConnectionSource.makeConnection(JdbcConnectionSource.java:252)
at com.j256.ormlite.jdbc.JdbcConnectionSource.getReadWriteConnection(JdbcConnectionSource.java:184)
at com.j256.ormlite.table.TableUtils.doCreateTable(TableUtils.java:440)
at com.j256.ormlite.table.TableUtils.createTable(TableUtils.java:220)
at com.j256.ormlite.table.TableUtils.createTableIfNotExists(TableUtils.java:61)
at com.limetray.pos.dbmanagers.DAO.init(DAO.java:75)
at com.limetray.pos.dbmanagers.DAO.createDB(DAO.java:172)
at com.limetray.pos.controllers.MainApp.appInitialization(MainApp.java:91)
at com.limetray.pos.controllers.MainApp.init(MainApp.java:80)
at com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:841)
at com.sun.javafx.application.LauncherImpl.lambda$launchApplication$155(LauncherImpl.java:182)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.IllegalStateException: File corrupted in chunk 1703, expected check value 1190, got 2040 [1.4.191/6]
at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:773)
at org.h2.mvstore.Page.read(Page.java:667)
at org.h2.mvstore.Page.read(Page.java:195)
at org.h2.mvstore.MVStore.readPage(MVStore.java:1939)
at org.h2.mvstore.MVMap.readPage(MVMap.java:736)
at org.h2.mvstore.Page.getChildPage(Page.java:217)
at org.h2.mvstore.Cursor.min(Cursor.java:129)
at org.h2.mvstore.Cursor.hasNext(Cursor.java:36)
at org.h2.mvstore.MVStore.loadChunkMeta(MVStore.java:689)
at org.h2.mvstore.MVStore.readStoreHeader(MVStore.java:670)
at org.h2.mvstore.MVStore.(MVStore.java:353)
at org.h2.mvstore.MVStore$Builder.open(MVStore.java:2888)
at org.h2.mvstore.db.MVTableEngine$Store.open(MVTableEngine.java:154)
and
org.h2.jdbc.JdbcSQLException: General error: "java.lang.NullPointerException" [50000-178]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:344)
at org.h2.message.DbException.get(DbException.java:167)
at org.h2.message.DbException.convert(DbException.java:294)
at org.h2.engine.Database.openDatabase(Database.java:293)
at org.h2.engine.Database.<init>(Database.java:256)
at org.h2.engine.Engine.openSession(Engine.java:57)
at org.h2.engine.Engine.openSession(Engine.java:164)
at org.h2.engine.Engine.createSessionAndValidate(Engine.java:142)
at org.h2.engine.Engine.createSession(Engine.java:125)
at org.h2.server.TcpServerThread.run(TcpServerThread.java:150)
at java.lang.Thread.run(Thread.java:744)
Caused by: java.lang.NullPointerException
at org.h2.mvstore.DataUtils.parseMap(DataUtils.java:630)
at org.h2.mvstore.MVStore.openMap(MVStore.java:411)
at org.h2.mvstore.db.TransactionStore.<init>(TransactionStore.java:96)
at org.h2.mvstore.db.MVTableEngine$Store.<init>(MVTableEngine.java:161)
at org.h2.mvstore.db.MVTableEngine.init(MVTableEngine.java:94)
at org.h2.engine.Database.getPageStore(Database.java:2355)
at org.h2.engine.Database.open(Database.java:659)
at org.h2.engine.Database.openDatabase(Database.java:262)
I think both are related to db corruption issue which is there in H2. How should I avoid this issue ? If not, Can I recover my data ?
When shutting down the noo4j DB I receive this error:
[org.neo4j]: Exception when stopping org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource#45673f68 java.nio.DirectByteBuffer[pos=16 lim=1048576 cap=1048576], 1586985
java.lang.IllegalArgumentException: java.nio.DirectByteBuffer[pos=16 lim=1048576 cap=1048576], 1586985
at org.neo4j.test.impl.EphemeralFileSystemAbstraction$DynamicByteBuffer.put(EphemeralFileSystemAbstraction.java:966)
at org.neo4j.test.impl.EphemeralFileSystemAbstraction$EphemeralFileData.write(EphemeralFileSystemAbstraction.java:680)
at org.neo4j.test.impl.EphemeralFileSystemAbstraction$EphemeralFileChannel.write(EphemeralFileSystemAbstraction.java:488)
at org.neo4j.kernel.impl.nioneo.store.StoreFileChannel.write(StoreFileChannel.java:160)
at org.neo4j.kernel.impl.nioneo.store.CommonAbstractStore$1.perform(CommonAbstractStore.java:579)
at org.neo4j.kernel.impl.util.FileUtils.windowsSafeIOOperation(FileUtils.java:367)
at org.neo4j.kernel.impl.nioneo.store.CommonAbstractStore.close(CommonAbstractStore.java:572)
at org.neo4j.kernel.impl.nioneo.store.NeoStore.closeStorage(NeoStore.java:289)
at org.neo4j.kernel.impl.nioneo.store.CommonAbstractStore.close(CommonAbstractStore.java:552)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource.stop(NeoStoreXaDataSource.java:507)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.stop(LifeSupport.java:527)
at org.neo4j.kernel.lifecycle.LifeSupport.stop(LifeSupport.java:155)
at org.neo4j.kernel.impl.transaction.XaDataSourceManager.stop(XaDataSourceManager.java:185)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.stop(LifeSupport.java:527)
at org.neo4j.kernel.lifecycle.LifeSupport.stop(LifeSupport.java:155)
at org.neo4j.kernel.lifecycle.LifeSupport.shutdown(LifeSupport.java:185)
at org.neo4j.kernel.InternalAbstractGraphDatabase.shutdown(InternalAbstractGraphDatabase.java:822)
at org.neo4j.test.ImpermanentGraphDatabase.shutdown(ImpermanentGraphDatabase.java:170)
at org.springframework.data.neo4j.support.DelegatingGraphDatabase.shutdown(DelegatingGraphDatabase.java:270)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
at org.springframework.beans.factory.support.DisposableBeanAdapter.invokeCustomDestroyMethod(DisposableBeanAdapter.java:350)
at org.springframework.beans.factory.support.DisposableBeanAdapter.destroy(DisposableBeanAdapter.java:273)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.destroyBean(DefaultSingletonBeanRegistry.java:565)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.destroySingleton(DefaultSingletonBeanRegistry.java:541)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.destroySingleton(DefaultListableBeanFactory.java:870)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.destroySingletons(DefaultSingletonBeanRegistry.java:510)
at org.springframework.context.support.AbstractApplicationContext.destroyBeans(AbstractApplicationContext.java:908)
at org.springframework.context.support.AbstractApplicationContext.doClose(AbstractApplicationContext.java:884)
at org.springframework.context.support.AbstractApplicationContext$1.run(AbstractApplicationContext.java:804)
Caused by: java.lang.IllegalArgumentException
at java.nio.Buffer.position(Buffer.java:244)
at org.neo4j.test.impl.EphemeralFileSystemAbstraction$DynamicByteBuffer.put(EphemeralFileSystemAbstraction.java:962)
... 31 more
2014-11-20 18:31:03.775+0000 ERROR [org.neo4j]: Exception when stopping org.neo4j.kernel.impl.transaction.XaDataSourceManager#4fd91628 Component 'org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource#45673f68' failed to stop. Please see attached cause exception.
org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource#45673f68' failed to stop. Please see attached cause exception.
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.stop(LifeSupport.java:532)
at org.neo4j.kernel.lifecycle.LifeSupport.stop(LifeSupport.java:155)
at org.neo4j.kernel.impl.transaction.XaDataSourceManager.stop(XaDataSourceManager.java:185)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.stop(LifeSupport.java:527)
at org.neo4j.kernel.lifecycle.LifeSupport.stop(LifeSupport.java:155)
at org.neo4j.kernel.lifecycle.LifeSupport.shutdown(LifeSupport.java:185)
at org.neo4j.kernel.InternalAbstractGraphDatabase.shutdown(InternalAbstractGraphDatabase.java:822)
I assume it is caused by a timeout, as it only appears when instantiating a large number of nodes (> 100K). However, I do not find a way to set up any timeout using the setConfig/GraphDatabaseSettings APIs (unfortunately we cannot use a property file):
public GraphDatabaseService graphDatabaseService() {
GraphDatabaseService graphDb = new GraphDatabaseFactory()
.newEmbeddedDatabaseBuilder("db/my.db")
.setConfig( GraphDatabaseSettings.nodestore_mapped_memory_size, "10M" )
.newGraphDatabase();
Do you know what is the root cause of the issue and how to circumvent it?
Thanks
F.