Build deletion has bad performance when running on MySQL

org.springframework.jdbc.UncategorizedSQLException: Hibernate flushing: Could not execute JDBC batch update; uncategorized SQLException for SQL [insert into REPOSITORY_CHANGESET (BUILDRESULTSUMMARY_ID, VCS_LOCATION_ID, CHANGESET_ID, SKIPPED_COMMITS_COUNT, LIST_POSITION, BUILD_TRIGGER, REPOSITORY_CHANGESET_ID) values (?, ?, ?, ?, ?, ?, ?)]; SQL state [41000]; error code [1205]; Lock wait timeout exceeded; try restarting transaction; nested exception is java.sql.BatchUpdateException: Lock wait timeout exceeded; try restarting transaction
	at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:84)
	at org.springframework.orm.hibernate3.HibernateTransactionManager.convertJdbcAccessException(HibernateTransactionManager.java:811)
	at org.springframework.orm.hibernate3.HibernateTransactionManager.convertHibernateAccessException(HibernateTransactionManager.java:797)
	at org.springframework.orm.hibernate3.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:669)
	at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:757)
	at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:726)
	at sun.reflect.GeneratedMethodAccessor130.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:201)
	at com.sun.proxy.$Proxy27.commit(Unknown Source)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:478)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:272)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:95)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
	at com.sun.proxy.$Proxy61.updateResultSummaryWithBuildChanges(Unknown Source)
	at com.atlassian.bamboo.chains.ChainExecutionManagerImpl$2.getChainState(ChainExecutionManagerImpl.java:235)
	at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.tryStartChainState(ChainExecutionManagerImpl.java:278)
	at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.delayedStart(ChainExecutionManagerImpl.java:214)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
	at com.sun.proxy.$Proxy146.delayedStart(Unknown Source)
	at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$2$1$1$1.run(PlanExecutionManagerImpl.java:430)
	at com.atlassian.bamboo.util.CacheAwareness$2.call(CacheAwareness.java:83)
	at com.atlassian.bamboo.util.CacheAwareness$2.call(CacheAwareness.java:79)
	at com.atlassian.bamboo.util.CacheAwareness.whileReadingThroughCaches(CacheAwareness.java:101)
	at com.atlassian.bamboo.util.CacheAwareness.whileReadingThroughCaches(CacheAwareness.java:78)
	at com.atlassian.bamboo.util.CacheAwareness.whileReadingThroughCaches(CacheAwareness.java:118)
	at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$2$1$1.call(PlanExecutionManagerImpl.java:425)
	at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$2$1$1.call(PlanExecutionManagerImpl.java:417)
	at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312)
	at com.atlassian.bamboo.plan.PlanExecutionLockServiceImpl.lock(PlanExecutionLockServiceImpl.java:85)
	at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.doWithProcessLock(PlanExecutionManagerImpl.java:800)
	at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.access$300(PlanExecutionManagerImpl.java:129)
	at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$2$1.run(PlanExecutionManagerImpl.java:411)
	at com.atlassian.bamboo.utils.BambooRunnables$1.run(BambooRunnables.java:49)
	at com.atlassian.bamboo.security.ImpersonationHelper.runWith(ImpersonationHelper.java:31)
	at com.atlassian.bamboo.security.ImpersonationHelper.runWithSystemAuthority(ImpersonationHelper.java:20)
	at com.atlassian.bamboo.security.ImpersonationHelper$1.run(ImpersonationHelper.java:52)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.sql.BatchUpdateException: Lock wait timeout exceeded; try restarting transaction
	at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:2054)
	at com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:1467)
	at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeBatch(NewProxyPreparedStatement.java:1723)
	at org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:70)
	at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:268)
	at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:268)
	at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:184)
	at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)
	at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:51)
	at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1216)
	at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:383)
	at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:133)
	at org.springframework.orm.hibernate3.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:661)
	... 46 more
Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1078)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4120)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4052)
	at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2503)
	at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2664)
	at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2815)
	at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2155)
	at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2458)
	at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:2006)
	... 58 more

2015-10-14 19:22:00,639 DEBUG [AtlassianEvent::0-BAM::EVENTS:pool-3-thread-8] [UtilTimerStack] [143344ms] - DeletionServiceImpl.removePlan(XXXXXXXXXXXXX)
  [143236ms] - Remove result summaries
    [16866ms] - Remove test results
    [61256ms] - delete from COMMIT_FILES  where COMMIT_ID in   (select COMMIT_ID from USER_COMMIT where REPOSITORY_CHANGESET_ID in     (select REPOSITORY_CHANGESET_ID from REPOSITORY_CHANGESET where BUILDRESULTSUMMARY_ID in       (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)     )   )
    [7749ms] - delete from USER_COMMIT  where REPOSITORY_CHANGESET_ID in   (select REPOSITORY_CHANGESET_ID from REPOSITORY_CHANGESET where BUILDRESULTSUMMARY_ID in     (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)   )
    [355ms] - delete from BRS_CONSUMED_SUBSCRIPTION  where ARTIFACT_LINK_ID in   (select ARTIFACT_LINK_ID from BRS_ARTIFACT_LINK     where BUILDRESULTSUMMARY_ID in        (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)     OR PRODUCERJOBRESULT_ID in        (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)   ) OR CONSUMER_RESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)
    [206ms] - delete from BRS_ARTIFACT_LINK  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)     or PRODUCERJOBRESULT_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?) 
    [1011ms] - delete from RELEVANT_CHANGESETS  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [1022ms] - delete from REPOSITORY_CHANGESET  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [1ms] - delete from BUILDRESULTSUMMARY_LABEL  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [51274ms] - delete from BUILDRESULTSUMMARY_CUSTOMDATA  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [516ms] - delete from BRS_LINKEDJIRAISSUES  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [426ms] - delete from VARIABLE_CONTEXT  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [1655ms] - delete from VARIABLE_SUBSTITUTION  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [10ms] - delete from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ? and BUILD_TYPE <> 'CHAIN'
    [3ms] - delete from STAGE_VARIABLE_CONTEXT  where STAGERESULT_ID IN   (select STAGERESULT_ID from CHAIN_STAGE_RESULT where CHAINRESULT_ID in     (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)   )
    [763ms] - delete from CHAIN_STAGE_RESULT  where CHAINRESULT_ID IN (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)
    [1ms] - delete from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ? and BUILD_TYPE = 'CHAIN'
  [10ms] - De-indexing build "XXXXXXXXXXXXX"
  [15ms] - Remove plan particles and dependencies
  [18ms] - Remove plan variables
  [13ms] - Remove repositories and plan vcs history
  [7ms] - Remove Bandana Data
  [10ms] - Remove agent assignments
  [0ms] - delete Buildable
    [0ms] - DeletionServiceImpl.clearBuildDirectories()

2015-10-14 19:22:00,759 WARN [AtlassianEvent::0-BAM::EVENTS:pool-3-thread-8] [S3ArtifactHandlerConfigurator] S3 artifact handler was used, but AWS credentials are missing
2015-10-14 19:22:00,760 WARN [AtlassianEvent::0-BAM::EVENTS:pool-3-thread-8] [S3ArtifactHandler] S3 artifact handling won't work: bucket name is invalid: [null]
2015-10-14 19:22:00,762 INFO [AtlassianEvent::0-BAM::EVENTS:pool-3-thread-8] [DeletionServiceImpl] Deleting XXXXXXXXXXXXX
2015-10-14 19:24:20,420 DEBUG [14-IndexerService.indexer:pool-30-thread-1] [UtilTimerStack] [1ms] - com.atlassian.bonnie.LoggingReentrantLock.indexWriteLock
  [1ms] - com.atlassian.bonnie.LoggingReentrantLock.searcherRefreshLock

2015-10-14 19:24:20,437 DEBUG [AtlassianEvent::0-BAM::EVENTS:pool-3-thread-8] [UtilTimerStack] [139674ms] - DeletionServiceImpl.removePlan(XXXXXXXXXXXXX)
  [139656ms] - Remove result summaries
    [16079ms] - Remove test results
    [58804ms] - delete from COMMIT_FILES  where COMMIT_ID in   (select COMMIT_ID from USER_COMMIT where REPOSITORY_CHANGESET_ID in     (select REPOSITORY_CHANGESET_ID from REPOSITORY_CHANGESET where BUILDRESULTSUMMARY_ID in       (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)     )   )
    [8064ms] - delete from USER_COMMIT  where REPOSITORY_CHANGESET_ID in   (select REPOSITORY_CHANGESET_ID from REPOSITORY_CHANGESET where BUILDRESULTSUMMARY_ID in     (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)   )
    [358ms] - delete from BRS_CONSUMED_SUBSCRIPTION  where ARTIFACT_LINK_ID in   (select ARTIFACT_LINK_ID from BRS_ARTIFACT_LINK     where BUILDRESULTSUMMARY_ID in        (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)     OR PRODUCERJOBRESULT_ID in        (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)   ) OR CONSUMER_RESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)
    [200ms] - delete from BRS_ARTIFACT_LINK  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)     or PRODUCERJOBRESULT_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?) 
    [1014ms] - delete from RELEVANT_CHANGESETS  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [1011ms] - delete from REPOSITORY_CHANGESET  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [1ms] - delete from BUILDRESULTSUMMARY_LABEL  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [50600ms] - delete from BUILDRESULTSUMMARY_CUSTOMDATA  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [529ms] - delete from BRS_LINKEDJIRAISSUES  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [416ms] - delete from VARIABLE_CONTEXT  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [1681ms] - delete from VARIABLE_SUBSTITUTION  where BUILDRESULTSUMMARY_ID in   (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ?)
    [7ms] - delete from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ? and BUILD_TYPE <> 'CHAIN'
    [1ms] - delete from STAGE_VARIABLE_CONTEXT  where STAGERESULT_ID IN   (select STAGERESULT_ID from CHAIN_STAGE_RESULT where CHAINRESULT_ID in     (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)   )
    [771ms] - delete from CHAIN_STAGE_RESULT  where CHAINRESULT_ID IN (select BUILDRESULTSUMMARY_ID from BUILDRESULTSUMMARY where BUILD_KEY = ?)
    [1ms] - delete from BUILDRESULTSUMMARY where BUILDRESULTSUMMARY.BUILD_KEY = ? and BUILD_TYPE = 'CHAIN'
  [1ms] - De-indexing build "XXXXXXXXXXXXX"
  [3ms] - Remove plan particles and dependencies
  [1ms] - Remove plan variables
  [7ms] - Remove repositories and plan vcs history
  [1ms] - Remove Bandana Data
  [0ms] - Remove agent assignments
  [0ms] - delete Buildable
    [0ms] - DeletionServiceImpl.clearBuildDirectories()