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Crowd fails with SQL Error: 1205, SQLState: 41000. Any suggestions?

James Katsis
James Katsis July 26, 2011

Hi guys,

We use Crowd to authenticate for jira and confluence. We have had this issue about 3 times now which causes an outage. We can easily fix the issue by restarting crowd service and my sql service or simply restart the windows box. We really need a solution to prevent it from occuring again.


I have already confirmed that the ransaction-isolation = READ-COMMITTED is in the mysql install directory. We are running crowd 2.04 on Windows server 2003 and mysql version 5.1.47.

Any help would be appreciated.

http://confluence.atlassian.com/pages/viewpage.action?pageId=229179847

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2011-07-25 16:21:53,210 http-8095-90 INFO [integration.directory.connector.ApacheDS15] Performing user search: baseDN = dc=bts,dc=cgu,dc=com,dc=au - filter = (&(objectclass=inetorgperson)(cn=nick.haughton))
2011-07-25 16:21:53,866 http-8095-72 WARN [org.hibernate.util.JDBCExceptionReporter] SQL Error: 1205, SQLState: 41000
2011-07-25 16:21:53,866 http-8095-72 ERROR [org.hibernate.util.JDBCExceptionReporter] Lock wait timeout exceeded; try restarting transaction
2011-07-25 16:21:53,866 http-8095-72 ERROR [hibernate.event.def.AbstractFlushingEventListener] Could not synchronize database state with session
org.hibernate.exception.GenericJDBCException: Could not execute JDBC batch update
at org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:103)
at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:91)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:253)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:237)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:142)
at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
at org.springframework.orm.hibernate3.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:606)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:709)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:678)
at org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:321)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:116)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
at $Proxy14.searchPrincipals(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.codehaus.xfire.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:59)
at org.codehaus.xfire.service.binding.ServiceInvocationHandler.sendMessage(ServiceInvocationHandler.java:320)
at org.codehaus.xfire.service.binding.ServiceInvocationHandler$1.run(ServiceInvocationHandler.java:86)
at org.codehaus.xfire.service.binding.ServiceInvocationHandler.execute(ServiceInvocationHandler.java:134)
at org.codehaus.xfire.service.binding.ServiceInvocationHandler.invoke(ServiceInvocationHandler.java:109)
at org.codehaus.xfire.handler.HandlerPipeline.invoke(HandlerPipeline.java:131)
at org.codehaus.xfire.transport.DefaultEndpoint.onReceive(DefaultEndpoint.java:64)
at org.codehaus.xfire.transport.AbstractChannel.receive(AbstractChannel.java:38)
at org.codehaus.xfire.transport.http.XFireServletController.invoke(XFireServletController.java:304)
at org.codehaus.xfire.transport.http.XFireServletController.doService(XFireServletController.java:129)
at org.codehaus.xfire.transport.http.XFireServlet.doPost(XFireServlet.java:116)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:637)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:55)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:41)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:55)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:41)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:55)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:41)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at com.atlassian.johnson.filters.AbstractJohnsonFilter.doFilter(AbstractJohnsonFilter.java:71)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198)
at com.atlassian.crowd.console.filter.CrowdOpenSessionInViewFilter.doFilterInternal(CrowdOpenSessionInViewFilter.java:26)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at com.atlassian.gzipfilter.GzipFilter.doFilterInternal(GzipFilter.java:75)
at com.atlassian.gzipfilter.GzipFilter.doFilter(GzipFilter.java:51)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:183)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:138)
at com.atlassian.crowd.console.filter.CrowdDelegatingFilterProxy.doFilter(CrowdDelegatingFilterProxy.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:55)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:41)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454)
at java.lang.Thread.run(Thread.java:619)
Caused by: java.sql.BatchUpdateException: Lock wait timeout exceeded; try restarting transaction
at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:2007)
at com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:1443)
at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeBatch(NewProxyPreparedStatement.java:1723)
at org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:246)
... 79 more
2011-07-25 16:21:53,866 http-8095-72 ERROR [codehaus.xfire.handler.DefaultFaultHandler] Fault occurred!
org.springframework.jdbc.UncategorizedSQLException: Hibernate flushing: Could not execute JDBC batch update; uncategorized SQLException for SQL [update cwd_token set directory_id=?, entity_name=?, random_number=?, identifier_hash=?, random_hash=?, created_date=?, last_accessed_date=? where id=?]; 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.SQLStateSQLExceptionTranslator.translate(SQLStateSQLExceptionTranslator.java:124)
at org.springframework.orm.hibernate3.HibernateTransactionManager.convertJdbcAccessException(HibernateTransactionManager.java:750)
at org.springframework.orm.hibernate3.HibernateTransactionManager.convertHibernateAccessException(HibernateTransactionManager.java:736)
at org.springframework.orm.hibernate3.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:614)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:709)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:678)
at org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:321)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:116)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
at $Proxy14.searchPrincipals(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.codehaus.xfire.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:59)
at org.codehaus.xfire.service.binding.ServiceInvocationHandler.sendMessage(ServiceInvocationHandler.java:320)
at org.codehaus.xfire.service.binding.ServiceInvocationHandler$1.run(ServiceInvocationHandler.java:86)
at org.codehaus.xfire.service.binding.ServiceInvocationHandler.execute(ServiceInvocationHandler.java:134)
at org.codehaus.xfire.service.binding.ServiceInvocationHandler.invoke(ServiceInvocationHandler.java:109)
at org.codehaus.xfire.handler.HandlerPipeline.invoke(HandlerPipeline.java:131)
at org.codehaus.xfire.transport.DefaultEndpoint.onReceive(DefaultEndpoint.java:64)
at org.codehaus.xfire.transport.AbstractChannel.receive(AbstractChannel.java:38)
at org.codehaus.xfire.transport.http.XFireServletController.invoke(XFireServletController.java:304)
at org.codehaus.xfire.transport.http.XFireServletController.doService(XFireServletController.java:129)
at org.codehaus.xfire.transport.http.XFireServlet.doPost(XFireServlet.java:116)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:637)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:55)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:41)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:55)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:41)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:55)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:41)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at com.atlassian.johnson.filters.AbstractJohnsonFilter.doFilter(AbstractJohnsonFilter.java:71)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198)
at com.atlassian.crowd.console.filter.CrowdOpenSessionInViewFilter.doFilterInternal(CrowdOpenSessionInViewFilter.java:26)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at com.atlassian.gzipfilter.GzipFilter.doFilterInternal(GzipFilter.java:75)
at com.atlassian.gzipfilter.GzipFilter.doFilter(GzipFilter.java:51)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:183)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:138)
at com.atlassian.crowd.console.filter.CrowdDelegatingFilterProxy.doFilter(CrowdDelegatingFilterProxy.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:55)
at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:41)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454)
at java.lang.Thread.run(Thread.java:619)

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3 answers

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Colin Goudie
Colin Goudie
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July 26, 2011

What is the your connection url setting in crowd.cfg.xml? This is in the your crowd home directory.

Does it have the autoReconnect parameter?

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James Katsis
James Katsis July 28, 2011

Hi Colin, Yes it does. the following line exists in the crowd.cfg.xml

<property name="hibernate.connection.url">jdbc:mysql://localhost/crowd?autoReconnect=true&amp;characterEncoding=utf8&amp;useUnicode=true<

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James Katsis
James Katsis July 26, 2011

Hi Colin, We originally setup the my sql connection using the JIRA configuration tool, rather than the manual method. This means there is no dbconfig.xml in the jira home directory. Where are the settings stored? How can i tell if we have the <tt><validation-query>select 1</validation-query></tt> line in the database config? Can i just create a dbconfig.xml?

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Colin Goudie
Colin Goudie
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July 26, 2011

My first thought is that the jdbc settings are not using a validation query to keep the MySQL connection around.

See this page in the JIRA docs, it may lead you to the answer

http://confluence.atlassian.com/display/JIRA/Connecting+JIRA+to+MySQL#ConnectingJIRAtoMySQL-4.2ConnectingJIRAtoMySQLManually

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