I am having cassandra cluster of 12 nodes on EC2 running cassandra-0.8.2.
While compaction I got the following exception which caused Seed node to get down.
Below is the exception stack trace.
ERROR [CompactionExecutor:31] 2011-12-16 08:06:02,308 AbstractCassandraDaemon.java (line 139) Fatal exception in thread Thread[CompactionExecutor:31,1,main]
java.io.IOError: java.io.EOFException: EOF after 430959023 bytes out of 778986868
at org.apache.cassandra.io.sstable.SSTableIdentityIterator.(SSTableIdentityIterator.java:149)
at org.apache.cassandra.io.sstable.SSTableIdentityIterator.(SSTableIdentityIterator.java:90)
at org.apache.cassandra.io.sstable.SSTableIdentityIterator.(SSTableIdentityIterator.java:74)
at org.apache.cassandra.io.sstable.SSTableScanner$KeyScanningIterator.next(SSTableScanner.java:179)
at org.apache.cassandra.io.sstable.SSTableScanner$KeyScanningIterator.next(SSTableScanner.java:144)
at org.apache.cassandra.io.sstable.SSTableScanner.next(SSTableScanner.java:136)
at org.apache.cassandra.io.sstable.SSTableScanner.next(SSTableScanner.java:39)
at org.apache.commons.collections.iterators.CollatingIterator.set(CollatingIterator.java:284)
at org.apache.commons.collections.iterators.CollatingIterator.least(CollatingIterator.java:326)
at org.apache.commons.collections.iterators.CollatingIterator.next(CollatingIterator.java:230)
at org.apache.cassandra.utils.ReducingIterator.computeNext(ReducingIterator.java:69)
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:140)
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:135)
at org.apache.commons.collections.iterators.FilterIterator.setNextObject(FilterIterator.java:183)
at org.apache.commons.collections.iterators.FilterIterator.hasNext(FilterIterator.java:94)
at org.apache.cassandra.db.compaction.CompactionManager.doCompactionWithoutSizeEstimation(CompactionManager.java:569)
at org.apache.cassandra.db.compaction.CompactionManager.doCompaction(CompactionManager.java:506)
at org.apache.cassandra.db.compaction.CompactionManager$1.call(CompactionManager.java:141)
at org.apache.cassandra.db.compaction.CompactionManager$1.call(CompactionManager.java:107)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)
Caused by: java.io.EOFException: EOF after 430959023 bytes out of 778986868
at org.apache.cassandra.io.util.FileUtils.skipBytesFully(FileUtils.java:229)
at org.apache.cassandra.io.sstable.IndexHelper.skipIndex(IndexHelper.java:63)
at org.apache.cassandra.io.sstable.SSTableIdentityIterator.(SSTableIdentityIterator.java:141)
... 23 more
It says it is Caused by: java.io.EOFException:
Is it because of the corrupt sstables?
if it is, then how to remove or repair those sstables?
It looks like this is indeed caused by corrupt sstables (which may indicate a hardware problem). My recommendations:
Upgrade to the latest stable 0.8.x version of Cassandra. This will be a drop-in replacement for 0.8.2.
Run "nodetool scrub" on the machine having problems
Review http://www.datastax.com/docs/1.0/install/cluster_init -- I recommend two seed nodes per data center, but remember that a seed node is only consulted when restarting nodes, so it's not a big deal to have one down during normal operation
Related
I am getting an error for my Java-based test code snippet when I run it from a GCE instance (whereas it works fine from my local machine, with the right credentials).
I used to be able to run Pub/Sub code from GCE instances just a few months ago, but seems like no longer. Not sure if this is an ipv4/ipv6 issue, but I can't find any information out there on how to properly configure GCE instances now to work with Pub/Sub.
Not sure if this is the issue, but it seems like i can reach pubsub.googleapis.com with ping, but not ping6:
ping pubsub.googleapis.com
PING pubsub.googleapis.com (173.194.196.95) 56(84) bytes of data.
vs.
ping6 pubsub.googleapis.com
connect: Network is unreachable
For what it's worth, here's the full Java stack trace:
Exception in thread "main" java.util.concurrent.ExecutionException: com.google.api.gax.rpc.UnavailableException: io.grpc.StatusRuntimeException: UNAVAILABLE: io exception
at com.google.common.util.concurrent.AbstractFuture.getDoneValue(AbstractFuture.java:552)
at com.google.common.util.concurrent.AbstractFuture.get(AbstractFuture.java:533)
at com.google.common.util.concurrent.AbstractFuture$TrustedFuture.get(AbstractFuture.java:90)
at com.google.common.util.concurrent.ForwardingFuture.get(ForwardingFuture.java:62)
at PSPublish.main(PSPublish.java:149)
Caused by: com.google.api.gax.rpc.UnavailableException: io.grpc.StatusRuntimeException: UNAVAILABLE: io exception
at com.google.api.gax.rpc.ApiExceptionFactory.createException(ApiExceptionFactory.java:69)
at com.google.api.gax.grpc.GrpcApiExceptionFactory.create(GrpcApiExceptionFactory.java:72)
at com.google.api.gax.grpc.GrpcApiExceptionFactory.create(GrpcApiExceptionFactory.java:60)
at com.google.api.gax.grpc.GrpcExceptionCallable$ExceptionTransformingFuture.onFailure(GrpcExceptionCallable.java:97)
at com.google.api.core.ApiFutures$1.onFailure(ApiFutures.java:68)
at com.google.common.util.concurrent.Futures$CallbackListener.run(Futures.java:1070)
at com.google.common.util.concurrent.DirectExecutor.execute(DirectExecutor.java:30)
at com.google.common.util.concurrent.AbstractFuture.executeListener(AbstractFuture.java:1138)
at com.google.common.util.concurrent.AbstractFuture.addListener(AbstractFuture.java:707)
at com.google.common.util.concurrent.ForwardingListenableFuture.addListener(ForwardingListenableFuture.java:45)
at com.google.api.core.ApiFutureToListenableFuture.addListener(ApiFutureToListenableFuture.java:52)
at com.google.common.util.concurrent.Futures.addCallback(Futures.java:1051)
at com.google.api.core.ApiFutures.addCallback(ApiFutures.java:63)
at com.google.api.gax.grpc.GrpcExceptionCallable.futureCall(GrpcExceptionCallable.java:67)
at com.google.api.gax.rpc.AttemptCallable.call(AttemptCallable.java:86)
at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:69)
at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:304)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: io.grpc.StatusRuntimeException: UNAVAILABLE: io exception
at io.grpc.Status.asRuntimeException(Status.java:532)
at io.grpc.stub.ClientCalls$UnaryStreamToFuture.onClose(ClientCalls.java:482)
at io.grpc.PartialForwardingClientCallListener.onClose(PartialForwardingClientCallListener.java:39)
at io.grpc.ForwardingClientCallListener.onClose(ForwardingClientCallListener.java:23)
at io.grpc.ForwardingClientCallListener$SimpleForwardingClientCallListener.onClose(ForwardingClientCallListener.java:40)
at io.grpc.internal.CensusStatsModule$StatsClientInterceptor$1$1.onClose(CensusStatsModule.java:699)
at io.grpc.PartialForwardingClientCallListener.onClose(PartialForwardingClientCallListener.java:39)
at io.grpc.ForwardingClientCallListener.onClose(ForwardingClientCallListener.java:23)
at io.grpc.ForwardingClientCallListener$SimpleForwardingClientCallListener.onClose(ForwardingClientCallListener.java:40)
at io.grpc.internal.CensusTracingModule$TracingClientInterceptor$1$1.onClose(CensusTracingModule.java:397)
at io.grpc.internal.ClientCallImpl.closeObserver(ClientCallImpl.java:459)
at io.grpc.internal.ClientCallImpl.access$300(ClientCallImpl.java:63)
at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl.close(ClientCallImpl.java:546)
at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl.access$600(ClientCallImpl.java:467)
at io.grpc.internal.ClientCallImpl$ClientStreamListenerImpl$1StreamClosed.runInContext(ClientCallImpl.java:584)
at io.grpc.internal.ContextRunnable.run(ContextRunnable.java:37)
at io.grpc.internal.SerializingExecutor.run(SerializingExecutor.java:123)
... 6 more
Caused by: io.grpc.netty.shaded.io.netty.channel.AbstractChannel$AnnotatedSocketException: Network is unreachable: pubsub.googleapis.com/2607:f8b0:4001:c03:0:0:0:5f:443
at java.base/sun.nio.ch.Net.connect0(Native Method)
at java.base/sun.nio.ch.Net.connect(Net.java:482)
at java.base/sun.nio.ch.Net.connect(Net.java:474)
at java.base/sun.nio.ch.SocketChannelImpl.connect(SocketChannelImpl.java:694)
at io.grpc.netty.shaded.io.netty.util.internal.SocketUtils$3.run(SocketUtils.java:83)
at io.grpc.netty.shaded.io.netty.util.internal.SocketUtils$3.run(SocketUtils.java:80)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at io.grpc.netty.shaded.io.netty.util.internal.SocketUtils.connect(SocketUtils.java:80)
at io.grpc.netty.shaded.io.netty.channel.socket.nio.NioSocketChannel.doConnect(NioSocketChannel.java:312)
at io.grpc.netty.shaded.io.netty.channel.nio.AbstractNioChannel$AbstractNioUnsafe.connect(AbstractNioChannel.java:254)
at io.grpc.netty.shaded.io.netty.channel.DefaultChannelPipeline$HeadContext.connect(DefaultChannelPipeline.java:1366)
at io.grpc.netty.shaded.io.netty.channel.AbstractChannelHandlerContext.invokeConnect(AbstractChannelHandlerContext.java:545)
at io.grpc.netty.shaded.io.netty.channel.AbstractChannelHandlerContext.connect(AbstractChannelHandlerContext.java:530)
at io.grpc.netty.shaded.io.netty.handler.ssl.SslHandler.connect(SslHandler.java:716)
at io.grpc.netty.shaded.io.netty.channel.AbstractChannelHandlerContext.invokeConnect(AbstractChannelHandlerContext.java:545)
at io.grpc.netty.shaded.io.netty.channel.AbstractChannelHandlerContext.connect(AbstractChannelHandlerContext.java:530)
at io.grpc.netty.shaded.io.netty.channel.ChannelDuplexHandler.connect(ChannelDuplexHandler.java:50)
at io.grpc.netty.shaded.io.grpc.netty.ProtocolNegotiators$AbstractBufferingHandler.connect(ProtocolNegotiators.java:491)
at io.grpc.netty.shaded.io.netty.channel.AbstractChannelHandlerContext.invokeConnect(AbstractChannelHandlerContext.java:545)
at io.grpc.netty.shaded.io.netty.channel.AbstractChannelHandlerContext.connect(AbstractChannelHandlerContext.java:530)
at io.grpc.netty.shaded.io.netty.channel.ChannelDuplexHandler.connect(ChannelDuplexHandler.java:50)
at io.grpc.netty.shaded.io.grpc.netty.WriteBufferingAndExceptionHandler.connect(WriteBufferingAndExceptionHandler.java:136)
at io.grpc.netty.shaded.io.netty.channel.AbstractChannelHandlerContext.invokeConnect(AbstractChannelHandlerContext.java:545)
at io.grpc.netty.shaded.io.netty.channel.AbstractChannelHandlerContext.access$1000(AbstractChannelHandlerContext.java:38)
at io.grpc.netty.shaded.io.netty.channel.AbstractChannelHandlerContext$11.run(AbstractChannelHandlerContext.java:535)
at io.grpc.netty.shaded.io.netty.util.concurrent.AbstractEventExecutor.safeExecute(AbstractEventExecutor.java:163)
at io.grpc.netty.shaded.io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:404)
at io.grpc.netty.shaded.io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:474)
at io.grpc.netty.shaded.io.netty.util.concurrent.SingleThreadEventExecutor$5.run(SingleThreadEventExecutor.java:909)
at io.grpc.netty.shaded.io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30)
... 1 more
Caused by: java.net.SocketException: Network is unreachable
I can't find any information out there on how to properly configure GCE instances now to work with Pub/Sub.
There is no Pub/Sub-specific configuration necessary for GCE VMs to talk to the Pub/Sub service. This seems like a networking issue outside the scope of the Pub/Sub service.
We've been using SonarQube for a long time, upgraded over many versions and now executed the long awaited LTS upgrade from version 5.6.6 to 6.7. Unfortunately, the database migration failed due to an SQLException "The table 'project_measures' is full".
Are there any guidelines about what do in such a case?
Is it not okay to upgrade directly from version 5.6.6 to 6.7? Should I first upgrade to some other intermediate version? I thought LTS-to-LTS upgrades should work out fine...
2017.11.15 00:49:38 INFO web[][DbMigrations] #1218 'Delete orphan measures without component': success | time=16143ms
2017.11.15 00:49:38 INFO web[][DbMigrations] #1219 'Make column PROJECT_MEASURES.COMPONENT_UUID not nullable'...
2017.11.15 00:51:04 ERROR web[][DbMigrations] #1219 'Make column PROJECT_MEASURES.COMPONENT_UUID not nullable': failure | time=85651ms
2017.11.15 00:51:04 ERROR web[][DbMigrations] Executed DB migrations: failure | time=1502042ms
2017.11.15 00:51:04 ERROR web[][o.s.s.p.d.m.DatabaseMigrationImpl] DB migration failed | time=1502119ms
2017.11.15 00:51:04 ERROR web[][o.s.s.p.d.m.DatabaseMigrationImpl] DB migration ended with an exception
org.sonar.server.platform.db.migration.step.MigrationStepExecutionException: Execution of migration step #1219 'Make column PROJECT_MEASURES.COMPONENT_UUID not nullable' failed
at org.sonar.server.platform.db.migration.step.MigrationStepsExecutorImpl.execute(MigrationStepsExecutorImpl.java:79)
at org.sonar.server.platform.db.migration.step.MigrationStepsExecutorImpl.execute(MigrationStepsExecutorImpl.java:67)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.ReferencePipeline$Head.forEachOrdered(ReferencePipeline.java:590)
at org.sonar.server.platform.db.migration.step.MigrationStepsExecutorImpl.execute(MigrationStepsExecutorImpl.java:52)
at org.sonar.server.platform.db.migration.engine.MigrationEngineImpl.execute(MigrationEngineImpl.java:50)
at org.sonar.server.platform.db.migration.DatabaseMigrationImpl.doUpgradeDb(DatabaseMigrationImpl.java:105)
at org.sonar.server.platform.db.migration.DatabaseMigrationImpl.doDatabaseMigration(DatabaseMigrationImpl.java:80)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.IllegalStateException: Fail to execute ALTER TABLE project_measures MODIFY COLUMN component_uuid VARCHAR (50) NOT NULL
at org.sonar.server.platform.db.migration.step.DdlChange$Context.execute(DdlChange.java:97)
at org.sonar.server.platform.db.migration.step.DdlChange$Context.execute(DdlChange.java:77)
at org.sonar.server.platform.db.migration.step.DdlChange$Context.execute(DdlChange.java:117)
at org.sonar.server.platform.db.migration.version.v60.MakeComponentUuidNotNullOnMeasures.execute(MakeComponentUuidNotNullOnMeasures.java:40)
at org.sonar.server.platform.db.migration.step.DdlChange.execute(DdlChange.java:45)
at org.sonar.server.platform.db.migration.step.MigrationStepsExecutorImpl.execute(MigrationStepsExecutorImpl.java:75)
... 11 common frames omitted
Caused by: java.sql.SQLException: The table 'project_measures' is full
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:964)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2486)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2444)
at com.mysql.jdbc.StatementImpl.executeInternal(StatementImpl.java:845)
at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:745)
at org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
at org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
at org.sonar.server.platform.db.migration.step.DdlChange$Context.execute(DdlChange.java:82)
... 16 common frames omitted
SonarQube is installed on a RHEL7 host using MySQL (rh-mysql57-mysql-server). The database location is /var/opt/rh/rh-mysql57/lib/mysql/sonar and there is free disk space available (but maybe not enough?):
/dev/mapper/vg0-var_opt 20G 17G 3.1G 85% /var/opt
Upgrade 5.6.6 to 6.7 is supported. According to your stack trace you are using MySQL server.
Can you have a look at server log files and the free space available on MySQL (maybe there is no enough space on your MySQL server for the migration) ?
Trying to run a simple hdfs query failed with:
[ms#cosmosmaster-gi ~]$ hadoop fs -ls /user/ms/def_serv/def_servpath
Java HotSpot(TM) 64-Bit Server VM warning: Insufficient space for shared memory file:
/tmp/hsperfdata_ms/21066
Try using the -Djava.io.tmpdir= option to select an alternate temp location.
Exception in thread "main" java.lang.NoClassDefFoundError: ___/tmp/hsperfdata_ms/21078
Caused by: java.lang.ClassNotFoundException: ___.tmp.hsperfdata_ms.21078
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
Could not find the main class: ___/tmp/hsperfdata_ms/21078. Program will exit.
Any idea how to fix that or increase quota?
Thanks!
ms
Your quota has not been exceeded (see command below), but this was a problem with the cluster. It should be fixed now.
$ hadoop fs -dus /user/ms
hdfs://cosmosmaster-gi/user/ms 90731
We are using JBoss 5.1 w/ MDB backed by ActiveMQ RAR.
When a message on a queue is consumed and performs some database operations which then result in a deadlock, the deadlock is essentially hosing the entire instance of JBoss until it is restarted. By hosed, any subsequent messages consumed on that queue all fail with the follow exception:
Caused by: javax.persistence.PersistenceException: org.hibernate.exception.GenericJDBCException: Cannot open connection
The deadlock exception never references my code, which in turn make it very difficult for me to catch and handle.
For example, here is an exception of a deadlock exception:
2012-06-18 18:52:19,848 WARN [JDBCExceptionReporter] : SQL Error: 1213, SQLState: 40001
2012-06-18 18:52:19,848 ERROR [JDBCExceptionReporter] : Deadlock found when trying to get lock; try restarting transaction
2012-06-18 18:52:19,850 ERROR [AbstractFlushingEventListener] : Could not synchronize database state with session
org.hibernate.exception.LockAcquisitionException: Could not execute JDBC batch update
at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:105)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:275)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:266)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:168)
at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)
at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1027)
at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:365)
at org.hibernate.ejb.AbstractEntityManagerImpl$1.beforeCompletion(AbstractEntityManagerImpl.java:504)
at com.arjuna.ats.internal.jta.resources.arjunacore.SynchronizationImple.beforeCompletion(SynchronizationImple.java:101)
at com.arjuna.ats.arjuna.coordinator.TwoPhaseCoordinator.beforeCompletion(TwoPhaseCoordinator.java:269)
at com.arjuna.ats.arjuna.coordinator.TwoPhaseCoordinator.end(TwoPhaseCoordinator.java:89)
at com.arjuna.ats.arjuna.AtomicAction.commit(AtomicAction.java:177)
at com.arjuna.ats.internal.jta.transaction.arjunacore.TransactionImple.commitAndDisassociate(TransactionImple.java:1423)
at com.arjuna.ats.internal.jta.transaction.arjunacore.BaseTransaction.commit(BaseTransaction.java:137)
at com.arjuna.ats.jbossatx.BaseTransactionManagerDelegate.commit(BaseTransactionManagerDelegate.java:75)
at org.jboss.ejb3.mdb.inflow.MessageInflowLocalProxy.endTransaction(MessageInflowLocalProxy.java:435)
at org.jboss.ejb3.mdb.inflow.MessageInflowLocalProxy.finish(MessageInflowLocalProxy.java:314)
at org.jboss.ejb3.mdb.inflow.MessageInflowLocalProxy.after(MessageInflowLocalProxy.java:230)
at org.jboss.ejb3.mdb.inflow.MessageInflowLocalProxy.invoke(MessageInflowLocalProxy.java:136)
at $Proxy677.afterDelivery(Unknown Source)
at org.apache.activemq.ra.MessageEndpointProxy$MessageEndpointAlive.afterDelivery(MessageEndpointProxy.java:128)
at org.apache.activemq.ra.MessageEndpointProxy.afterDelivery(MessageEndpointProxy.java:69)
at org.apache.activemq.ra.ServerSessionImpl.afterDelivery(ServerSessionImpl.java:224)
at org.apache.activemq.ActiveMQSession.run(ActiveMQSession.java:897)
at org.apache.activemq.ra.ServerSessionImpl.run(ServerSessionImpl.java:169)
at org.jboss.resource.work.WorkWrapper.execute(WorkWrapper.java:205)
at org.jboss.util.threadpool.BasicTaskWrapper.run(BasicTaskWrapper.java:260)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:619)
Caused by: java.sql.BatchUpdateException: Deadlock found when trying to get lock; try restarting transaction
at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:2013)
at com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:1449)
at com.mysql.jdbc.jdbc2.optional.StatementWrapper.executeBatch(StatementWrapper.java:721)
at org.jboss.resource.adapter.jdbc.WrappedStatement.executeBatch(WrappedStatement.java:774)
at org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:70)
at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:268)
... 29 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLTransactionRollbackException: Deadlock found when trying to get lock; try restarting transaction
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:407)
at com.mysql.jdbc.Util.getInstance(Util.java:382)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1064)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3603)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3535)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1989)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2150)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2626)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2119)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2415)
at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:1976)
... 34 more
2012-06-18 18:52:19,851 WARN [arjLoggerI18N] : [com.arjuna.ats.arjuna.coordinator.TwoPhaseCoordinator_2] TwoPhaseCoordinator.beforeCompletion - failed for com.arjuna.ats.internal.jta.resources.arjunacore.SynchronizationImple#480671ab
javax.persistence.PersistenceException: org.hibernate.exception.LockAcquisitionException: Could not execute JDBC batch update
at org.hibernate.ejb.AbstractEntityManagerImpl.throwPersistenceException(AbstractEntityManagerImpl.java:614)
at org.hibernate.ejb.AbstractEntityManagerImpl$1.beforeCompletion(AbstractEntityManagerImpl.java:513)
at com.arjuna.ats.internal.jta.resources.arjunacore.SynchronizationImple.beforeCompletion(SynchronizationImple.java:101)
at com.arjuna.ats.arjuna.coordinator.TwoPhaseCoordinator.beforeCompletion(TwoPhaseCoordinator.java:269)
at com.arjuna.ats.arjuna.coordinator.TwoPhaseCoordinator.end(TwoPhaseCoordinator.java:89)
at com.arjuna.ats.arjuna.AtomicAction.commit(AtomicAction.java:177)
at com.arjuna.ats.internal.jta.transaction.arjunacore.TransactionImple.commitAndDisassociate(TransactionImple.java:1423)
at com.arjuna.ats.internal.jta.transaction.arjunacore.BaseTransaction.commit(BaseTransaction.java:137)
at com.arjuna.ats.jbossatx.BaseTransactionManagerDelegate.commit(BaseTransactionManagerDelegate.java:75)
at org.jboss.ejb3.mdb.inflow.MessageInflowLocalProxy.endTransaction(MessageInflowLocalProxy.java:435)
at org.jboss.ejb3.mdb.inflow.MessageInflowLocalProxy.finish(MessageInflowLocalProxy.java:314)
at org.jboss.ejb3.mdb.inflow.MessageInflowLocalProxy.after(MessageInflowLocalProxy.java:230)
at org.jboss.ejb3.mdb.inflow.MessageInflowLocalProxy.invoke(MessageInflowLocalProxy.java:136)
at $Proxy677.afterDelivery(Unknown Source)
at org.apache.activemq.ra.MessageEndpointProxy$MessageEndpointAlive.afterDelivery(MessageEndpointProxy.java:128)
at org.apache.activemq.ra.MessageEndpointProxy.afterDelivery(MessageEndpointProxy.java:69)
at org.apache.activemq.ra.ServerSessionImpl.afterDelivery(ServerSessionImpl.java:224)
at org.apache.activemq.ActiveMQSession.run(ActiveMQSession.java:897)
at org.apache.activemq.ra.ServerSessionImpl.run(ServerSessionImpl.java:169)
at org.jboss.resource.work.WorkWrapper.execute(WorkWrapper.java:205)
at org.jboss.util.threadpool.BasicTaskWrapper.run(BasicTaskWrapper.java:260)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:619)
Caused by: org.hibernate.exception.LockAcquisitionException: Could not execute JDBC batch update
at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:105)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:275)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:266)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:168)
at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)
at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1027)
at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:365)
at org.hibernate.ejb.AbstractEntityManagerImpl$1.beforeCompletion(AbstractEntityManagerImpl.java:504)
... 22 more
Caused by: java.sql.BatchUpdateException: Deadlock found when trying to get lock; try restarting transaction
at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:2013)
at com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:1449)
at com.mysql.jdbc.jdbc2.optional.StatementWrapper.executeBatch(StatementWrapper.java:721)
at org.jboss.resource.adapter.jdbc.WrappedStatement.executeBatch(WrappedStatement.java:774)
at org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:70)
at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:268)
... 29 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLTransactionRollbackException: Deadlock found when trying to get lock; try restarting transaction
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:407)
at com.mysql.jdbc.Util.getInstance(Util.java:382)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1064)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3603)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3535)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1989)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2150)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2626)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2119)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2415)
at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:1976)
... 34 more
2012-06-18 18:52:19,912 WARN [TxConnectionManager] : Connection error occured: org.jboss.resource.connectionmanager.TxConnectionManager$TxConnectionEventListener#6acc2da9[state=NORMAL mc=org.jboss.resource.adapter.jdbc.xa.XAManagedConnection#2c9e906 handles=0 lastUse=1340059939649 permit=true trackByTx=true mcp=org.jboss.resource.connectionmanager.JBossManagedConnectionPool$OnePool#10015060 context=org.jboss.resource.connectionmanager.InternalManagedConnectionPool#4643d6d5 xaResource=org.jboss.resource.adapter.jdbc.xa.XAManagedConnection#2c9e906 txSync=null]
com.mysql.jdbc.jdbc2.optional.MysqlXAException: XA_RBDEADLOCK: Transaction branch was rolled back: deadlock was detected
at com.mysql.jdbc.jdbc2.optional.MysqlXAConnection.mapXAExceptionFromSQLException(MysqlXAConnection.java:605)
at com.mysql.jdbc.jdbc2.optional.MysqlXAConnection.dispatchCommand(MysqlXAConnection.java:584)
at com.mysql.jdbc.jdbc2.optional.MysqlXAConnection.end(MysqlXAConnection.java:479)
at org.jboss.resource.adapter.jdbc.xa.XAManagedConnection.end(XAManagedConnection.java:246)
at com.arjuna.ats.internal.jta.resources.arjunacore.XAResourceRecord.topLevelAbort(XAResourceRecord.java:396)
at com.arjuna.ats.arjuna.coordinator.BasicAction.doAbort(BasicAction.java:3270)
at com.arjuna.ats.arjuna.coordinator.BasicAction.doAbort(BasicAction.java:3248)
at com.arjuna.ats.arjuna.coordinator.BasicAction.Abort(BasicAction.java:1933)
at com.arjuna.ats.arjuna.coordinator.TwoPhaseCoordinator.end(TwoPhaseCoordinator.java:97)
at com.arjuna.ats.arjuna.AtomicAction.commit(AtomicAction.java:177)
at com.arjuna.ats.internal.jta.transaction.arjunacore.TransactionImple.commitAndDisassociate(TransactionImple.java:1423)
at com.arjuna.ats.internal.jta.transaction.arjunacore.BaseTransaction.commit(BaseTransaction.java:137)
at com.arjuna.ats.jbossatx.BaseTransactionManagerDelegate.commit(BaseTransactionManagerDelegate.java:75)
at org.jboss.ejb3.mdb.inflow.MessageInflowLocalProxy.endTransaction(MessageInflowLocalProxy.java:435)
at org.jboss.ejb3.mdb.inflow.MessageInflowLocalProxy.finish(MessageInflowLocalProxy.java:314)
at org.jboss.ejb3.mdb.inflow.MessageInflowLocalProxy.after(MessageInflowLocalProxy.java:230)
at org.jboss.ejb3.mdb.inflow.MessageInflowLocalProxy.invoke(MessageInflowLocalProxy.java:136)
at $Proxy677.afterDelivery(Unknown Source)
at org.apache.activemq.ra.MessageEndpointProxy$MessageEndpointAlive.afterDelivery(MessageEndpointProxy.java:128)
at org.apache.activemq.ra.MessageEndpointProxy.afterDelivery(MessageEndpointProxy.java:69)
at org.apache.activemq.ra.ServerSessionImpl.afterDelivery(ServerSessionImpl.java:224)
at org.apache.activemq.ActiveMQSession.run(ActiveMQSession.java:897)
at org.apache.activemq.ra.ServerSessionImpl.run(ServerSessionImpl.java:169)
at org.jboss.resource.work.WorkWrapper.execute(WorkWrapper.java:205)
at org.jboss.util.threadpool.BasicTaskWrapper.run(BasicTaskWrapper.java:260)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:619)
2012-06-18 18:52:19,914 INFO [ServerSessionImpl:153] : Endpoint failed to process message. Reason: Endpoint after delivery notification failure
I can catch the subsequent errors (the errors on subsequent messages to the queue):
Caused by: javax.persistence.PersistenceException: org.hibernate.exception.GenericJDBCException: Cannot open connection
But I'm not even sure what to do with it, maybe I can get a new EntityManager that isn't hosed, but I'm getting via Injection to begin with... The only way I know to fix this error is to restart.
I assume that the initial Deadlock is happening as part of ending the transaction in the Queue which is why it's not happening in my code, but does any idea of a way I can handle this gracefully?
Update:
All DataSources are MySQL XA
In transaction-jboss-beans.xml we have transactionTimeout set to 300
There is no way to handle container transaction exception gracefully.
It decides to rollback whatever the reason is and you have no control against it. A complex option to get notified about such exceptions and rollback events may be to write a JCA connector which enrolls fake resources into the distributed transaction manager for each MDB transaction.
I would recommend you to investigate what happens and fix the trouble from its source.
Here is a dead-lock scenario, it always involve multiple threads: if two pieces of code use the same entities but in different order, a first thread will lock resource A (a row, a table or a Java monitor) and wait for B when a second thread have already locked resource B and now waits for A.
So a distributed dead-lock is possible between Java monitors and Database resources and that case is complex to diagnose. The full system is stuck until the transaction timeouts at both ends, Java thread dumps and database sessions and locks must be scanned.
In your case, as MySQL detects the dead-lock itself, it means only database resources are involved.
To help, I guess you should reduce the number of SQL queries run in your batch update for one JMS message, one transaction. With concurrent messages consumed at the same time, working on transaction applying large number of rows, a deadlock situation is more likely to occur.
But it is strange that your JBoss server is stuck after rollback because of a DB-only dead-lock:
either you have exhausted the number of JDBC connections from the DataSource pool
or there is no more MySQL server-side connection available
or all message beans are in dead-lock situation too
the transaction timeout may be too high to get rollbacks in a reasonable time frame
So either you reduce MDB concurrency by down sizing the corresponding pool, either you reduce the number of updates per transaction - maybe even as small as one update per JMS message...
I was able to resolve this by isolating each transaction using the following method:
Annotate the MDB with:
#TransactionManagement(value = TransactionManagementType.BEAN)
Thus telling the MDB that the Bean itself will manage the transaction and not the container (outside of my code), next, inject the necessary resources:
#Resource
MessageDrivenContext mc;
UserTransaction tx;
To create and manage my own transactions
tx = mc.getUserTransaction();
tx.begin();
//Do work
tx.commit();
The above step can be repeated for each block of code.
Using very granular transactions I was able to trace where in my code the lock / race condition was happening. Once I solved that I was able to back out some of the more granular transaction management.
hibernate 3.6.8 final
c3p0 jar that came with hibernate 3.6.8 package -> c3p0-0.9.1.jar
1
15
40
0
5
2
The app seems to be working fine, however I get massive log calls with the following stacktrace:
org.apache.catalina.loader.WebappClassLoader loadClass
INFO: Illegal access: this web application instance has been stopped already. Could not load com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException. The eventual following stack trace is caused by an error thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access, and has no functional impact.
java.lang.IllegalStateException
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1566)
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1526)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:169)
at com.mysql.jdbc.Util.getInstance(Util.java:386)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1013)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:987)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:982)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:927)
at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2411)
at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2153)
at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:792)
at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
at sun.reflect.GeneratedConstructorAccessor38.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:381)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:305)
at com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:134)
at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:182)
at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:171)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.acquireResource(C3P0PooledConnectionPool.java:152)
at com.mchange.v2.resourcepool.BasicResourcePool.doAcquire(BasicResourcePool.java:1074)
at com.mchange.v2.resourcepool.BasicResourcePool.doAcquireAndDecrementPendingAcquiresWithinLockOnSuccess(BasicResourcePool.java:1061)
at com.mchange.v2.resourcepool.BasicResourcePool.access$800(BasicResourcePool.java:32)
at com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask.run(BasicResourcePool.java:1796)
at com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:620)
Any information on how to remove that INFO log would be very much helpful thanks!
UPDATE: Is this a critical error? Or can should I just ignore it?
After a search on the web regarding this issue, I found some similar issues reported by several people. All of them point to a common problem: Threads. Basically, if you start new threads in your application (either in your code or by using a third party tool like Quartz, you have to make sure that all of the threads are stopped appropriately when the application is undeployed from the server. Here are some quotes from the searches:
Mikolaj Rydzewski wrote:
It looks like after webapp's instance has been undeployed, background quartz thread wants to do something and then exception occurs.
Another (and better explanation) on jspwiki.org:
It is possible that this is caused by Tomcat unsuccessfully reloading the web application. The app is unloaded, but all threads don't get shut down properly. As a result, when the threads try to run, they get clobbered by the fact that Tomcat has shut down its classloader, and an error is logged.
So, in order to solve this issue you have to make sure all threads started by your application will be stopped at application undeployment (or redeployment, it's the same). You can do this by registering a ServletContextListener to your application server and stopping your threads inside contextDestroyed(ServletContextEvent) method.
If you are using log4j, change your logging settings to something like this (the word ERROR replace INFO) :
log4j.rootLogger=ERROR, file, stdout
log4j.logger.org.hibernate=ERROR
They are located in the the log4j.properties file in yr project.
OK I switched to boneCP, c3p0 does not really seem to work for java6!!!