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Java multi threaded application - getting "Bad File Descriptor" exception on Hive intermittently

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

OPC client issue

I am getting the following error in the OPC client code.
I start my client- close it - start it again to see the following error.
It is clear that something from previous run is causing it. But I am unable to figure out what it is.
When I diff the jstack of my first run and close. I do not see any running thread from opc.
Has anyone seen this issue? Or
Is there some other way I can debug the issue?
2016-05-19 16:35:53,564 WARN [netty-event-loop-0] io.netty.channel.ChannelInitializer - Failed to initialize a channel. Closing: [id: 0xe25cac5b] java.lang.ExceptionInInitializerError
at com.digitalpetri.opcua.stack.client.UaTcpStackClient$1.initChannel(UaTcpStackClient.java:340)
at com.digitalpetri.opcua.stack.client.UaTcpStackClient$1.initChannel(UaTcpStackClient.java:337)
at io.netty.channel.ChannelInitializer.channelRegistered(ChannelInitializer.java:69)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRegistered(AbstractChannelHandlerContext.java:133)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRegistered(AbstractChannelHandlerContext.java:119)
at io.netty.channel.DefaultChannelPipeline.fireChannelRegistered(DefaultChannelPipeline.java:733)
at io.netty.channel.AbstractChannel$AbstractUnsafe.register0(AbstractChannel.java:449)
at io.netty.channel.AbstractChannel$AbstractUnsafe.access$100(AbstractChannel.java:377)
at io.netty.channel.AbstractChannel$AbstractUnsafe$1.run(AbstractChannel.java:423)
at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:380)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:357)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116)
at java.lang.Thread.run(Thread.java:745) Caused by: java.lang.IllegalArgumentException: 'awaiting-handshake' is already in use
at io.netty.util.UniqueName.<init>(UniqueName.java:53)
at io.netty.util.AttributeKey.<init>(AttributeKey.java:47)
at io.netty.util.AttributeKey.valueOf(AttributeKey.java:39)
at com.digitalpetri.opcua.stack.client.handlers.UaTcpClientAcknowledgeHandler.<clinit>(UaTcpClientAcknowledgeHandler.java:44)
... 13 more

Looks like you might have some kind of ClassLoader issue - a static final field of UaTcpAcknowledgeHandler is being defined twice somehow.
What exactly happens when you "close" your client?

NullPointerException in Camus Job [EtlMultiOutputRecordWriter] - ExceptionWritable

I am very new to Camus and Hadoop, and am running into an exception error. I am trying to write some avro files to a hdfs, and keep getting the following error block:
[EtlMultiOutputRecordWriter] - ExceptionWritable key: topic=_schemas partition=0leaderId=0 server= service= beginOffset=0 offset=0 msgSize=1024 server= checksum=0 time=1450371931447 value: java.lang.Exception
at com.linkedin.camus.etl.kafka.common.KafkaReader.getNext(KafkaReader.java:108)
at com.linkedin.camus.etl.kafka.mapred.EtlRecordReader.nextKeyValue(EtlRecordReader.java:232)
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:145)
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.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:243)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NullPointerException
... 14 more
I looked up line 108 in com.linkedin.camus.etl.kafka.common.KafkaReader.getNext and found it to be this: MessageAndOffset msgAndOffset = messageIter.next();.
I am using io.confluent.camus.etl.kafka.coders.AvroMessageDecoder for my decoder and com.linkedin.camus.example.DummySchemaRegistry for my coder.
At the end of the logs I get another line indicating an error from one of the hdfs files: Error from file [hdfs://localhost:9000/user/username/exec/2015-12-17-17-05-25/errors-m-00000]. The error-m-00000 file contains a somewhat readable beginning, but then changes to an undecipherable string:
SEQ*com.linkedin.camus.etl.kafka.common.EtlKey5com.linkedin.camus.etl.kafka.common.ExceptionWritable*org.apache.hadoop.io.compress.DefaultCodec|Ò ∫±ß˝}pºHí$ò¸·:0schemasQ∞∆øÿxúïîÀN√0E7l‡+∫»¢lFMõ>á*êxU®™ËzÍmàc[ÆÕ„XÚÕÿqZ%#[ÿD±gÓô…¯∆üGœ¯Ç¿Q,·Úçë2ô'«hZL¿3ëSöXÿ5ê·ê„Sé‡ÇÖpÎS¬î4,…LËÕ¥Î{û}wFßáâ*M)>%&uZÑCfi“˚#rKÌÔ¡flÌu^Í%†B∂"Xa*•⁄0ÔQÕpùGzùidy&ñªkT…śԈ≥-#0>›…∆RG∫.ˇÅ¨«JÚ®sÃ≥Ö¡\£Rîfi˚ßéT≥D#%T8ãW®ÚµÌ∫4N˙©W∫©mst√—Ô嶥óhÓ$C~#S+Ñâ{ãÇfl¡ßí⁄L´ÏíÙºÙΩ5wfÃjM¬∏_Äò5RØ£
Ë"Eeúÿëx{ÆÏ«{XW÷XM€O¨-C#É¡Òl•ù9§‰õö2ó:wɲ%Œ-N∫ˇbFXˆ∑:àá5fyQÑ‘ö™:roõ1⁄5•≠≈˚yM0±ú?»ÃW◊.h≈I´êöNæ
[û3
At the end it appears that a hadoop job has run, but a commit never takes place, based of the timing report:
Job time (seconds):
pre setup 1.0 (11%)
get splits 1.0 (11%)
hadoop job 4.0 (44%)
commit 0.0 (0%)
Total: 0 minutes 9 seconds
Any help or an idea of where to look to resolve this would be greatly appreciated. Thank you.

Neo4j kernel crashing when loading large graph

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.

odd SQLException - Could not retrieve transation read-only status server

I have a Quartz Job that executes a Stored Procedure in my MySQL database once every 5 minutes, and for some reason, 1 out of 3 executions fails and gives this weird exception. I have searched and searched for what this exception means, but I could not find a solution. Here is the full stack trace:
java.sql.SQLException: Could not retrieve transation read-only status server
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1078)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:989)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:975)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:920)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:951)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:941)
at com.mysql.jdbc.ConnectionImpl.isReadOnly(ConnectionImpl.java:3939)
at com.mysql.jdbc.ConnectionImpl.isReadOnly(ConnectionImpl.java:3910)
at com.mysql.jdbc.PreparedStatement.checkReadOnlySafeStatement(PreparedStatement.java:1258)
at com.mysql.jdbc.CallableStatement.checkReadOnlySafeStatement(CallableStatement.java:2656)
at com.mysql.jdbc.PreparedStatement.execute(PreparedStatement.java:1278)
at com.mysql.jdbc.CallableStatement.execute(CallableStatement.java:920)
at com.mchange.v2.c3p0.impl.NewProxyCallableStatement.execute(NewProxyCallableStatement.java:3044)
at org.deadmandungeons.website.tasks.RankUpdateTask.execute(RankUpdateTask.java:30)
at org.quartz.core.JobRunShell.run(JobRunShell.java:202)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:573)
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
The last packet successfully received from the server was 1,198,219 milliseconds ago. The last packet sent successfully to the server was 950,420 milliseconds ago.
at sun.reflect.GeneratedConstructorAccessor43.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1121)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3673)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3562)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4113)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2570)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2731)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2812)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2761)
at com.mysql.jdbc.StatementImpl.executeQuery(StatementImpl.java:1612)
at com.mysql.jdbc.ConnectionImpl.isReadOnly(ConnectionImpl.java:3933)
... 9 more
Caused by: java.net.SocketException: Connection timed out
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(SocketInputStream.java:150)
at java.net.SocketInputStream.read(SocketInputStream.java:121)
at com.mysql.jdbc.util.ReadAheadInputStream.fill(ReadAheadInputStream.java:114)
at com.mysql.jdbc.util.ReadAheadInputStream.readFromUnderlyingStreamIfNecessary(ReadAheadInputStream.java:161)
at com.mysql.jdbc.util.ReadAheadInputStream.read(ReadAheadInputStream.java:189)
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:3116)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3573)
... 17 more
So I figured it is timing out because it thinks the MySQL server is in read-only status?
This only happens for this quartz job, and not any other time when I communicate with the database. This execution is of course happening in another thread, but I don't think that would have anything to do with it.
Why would it think the server was in read-only mode?
Also, I don't think "transation" is a word, so there's that...

Sorry for posting on old thread,
As stack trace says
com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
This implies the link between JDBC and DB is broken.As per your observation you say 1 out of 3 job invocations fails.
You have these jobs scheduled every 5 minutes and as per trace the last successful message sent to server is ~15 minutes before.
Hence I suspect either
You are procedure is not returning (waiting on something)
The JDBC connection has been invalidated by the firewall/ proxy
It will interesting to see the how connections are managed, As per logs I see you are using c3p0.
You can try setting unreturnedConnectionTimeout and debugUnreturnedConnectionStackTraces. This will give you more insight into connection leaks or db calls which are taking long.

Research takes nowhere, as you guys said, but the error shows what seems to be a Database being populated by two applications at the same time.
Do you have admin privileges on this MySQL server? If you do, you should try setting
FLUSH TABLES WITH READ LOCK;
SET GLOBAL READ_ONLY=ON;
as a test to reproduce the error. Just to warn you, this command makes your database unwritable, so you will not be able to add data in it until you revert this configuration, obviously with
SET GLOBAL READ_ONLY=0;
UNLOCK TABLES;
If the result of this test is positive (same error had been reproduced), you should try isolating applications that are storing data on your database, to find out which one is conflicting with Quartz.
I'm sorry for being vague, but I hope it gives you some help...