Google App Engine + Cloud SQL + Hibernate Broken pipe

Question

I have an app-engine+spring+hibernate mobile/web backend configured with F2 instances and D2 cloud sql instance. I've also configure warm-ups by configuring Idle Instances to be minimum 1.

From time to time in different requests I get the following exception. I couldn't figure out the pattern and the cause of this exception:

2.54.55.112 - - [19/Jul/2014:23:11:06 -0700] "GET /something HTTP/1.1" 500 0 - "Dalvik/1.6.0 (Linux; U; Android 4.4.2;.....)" "mybusiness.com" ms=487 cpu_ms=22208 app_engine_release=1.9.7 trace_id=
  I 09:11:05.885 .<stdout>: WARN : SQL Error: 0, SQLState: null  at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.(SqlExceptionHelper.java:144) on 2014-07-20 06:11:05,884

  I 09:11:05.886 .<stdout>: ERROR: Already closed.  at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.(SqlExceptionHelper.java:146) on 2014-07-20 06:11:05,885

  W 09:11:06.300 /something
org.springframework.transaction.CannotCreateTransactionException: Could not open Hibernate Session for transaction; nested exception is org.hibernate.TransactionException: JDBC begin transaction failed: 
at org.springframework.orm.hibernate4.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:515)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:373)
at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:420)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:257)
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.$Proxy18.loadEntityByIdNow(Unknown Source)
at com.mybusiness.web.authentication.MybusinessTokenRepository.getTokenForSeries(MybusinessTokenRepository.java:79)
at org.springframework.security.web.authentication.rememberme.PersistentTokenBasedRememberMeServices.processAutoLoginCookie(PersistentTokenBasedRememberMeServices.java:90)
at org.springframework.security.web.authentication.rememberme.AbstractRememberMeServices.autoLogin(AbstractRememberMeServices.java:115)
at org.springframework.security.web.authentication.rememberme.RememberMeAuthenticationFilter.doFilter(RememberMeAuthenticationFilter.java:97)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.ui.DefaultLoginPageGeneratingFilter.doFilter(DefaultLoginPageGeneratingFilter.java:155)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at com.google.apphosting.utils.servlet.ParseBlobUploadFilter.doFilter(ParseBlobUploadFilter.java:125)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at com.google.apphosting.runtime.jetty.SaveSessionFilter.doFilter(SaveSessionFilter.java:35)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at com.google.apphosting.utils.servlet.JdbcMySqlConnectionCleanupFilter.doFilter(JdbcMySqlConnectionCleanupFilter.java:60)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at com.google.apphosting.utils.servlet.TransactionCleanupFilter.doFilter(TransactionCleanupFilter.java:43)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
at com.google.apphosting.runtime.jetty.AppVersionHandlerMap.handle(AppVersionHandlerMap.java:254)
at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
at org.mortbay.jetty.Server.handle(Server.java:326)
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:923)
at com.google.apphosting.runtime.jetty.RpcRequestParser.parseAvailable(RpcRequestParser.java:76)
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
at com.google.apphosting.runtime.jetty.JettyServletEngineAdapter.serviceRequest(JettyServletEngineAdapter.java:146)
at com.google.apphosting.runtime.JavaRuntime$RequestRunnable.run(JavaRuntime.java:446)
at com.google.tracing.TraceContext$TraceContextRunnable.runInContext(TraceContext.java:437)
at com.google.tracing.TraceContext$TraceContextRunnable$1.run(TraceContext.java:444)
at com.google.tracing.CurrentContext.runInContext(CurrentContext.java:188)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContextNoUnref(TraceContext.java:308)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContext(TraceContext.java:300)
at com.google.tracing.TraceContext$TraceContextRunnable.run(TraceContext.java:441)
at com.google.apphosting.runtime.ThreadGroupPool$PoolEntry.run(ThreadGroupPool.java:251)
at java.lang.Thread.run(Thread.java:724)
Caused by: org.hibernate.TransactionException: JDBC begin transaction failed: 
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doBegin(JdbcTransaction.java:76)
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.begin(AbstractTransactionImpl.java:162)
at org.hibernate.internal.SessionImpl.beginTransaction(SessionImpl.java:1435)
at org.springframework.orm.hibernate4.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:474)
... 64 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 38,806,609 milliseconds ago.  The last packet sent successfully to the server was 38,806,611 milliseconds ago. is longer than the server configured value of 'wait_timeout'. You should consider either expiring and/or testing connection validity before use in your application, increasing the server configured values for client timeouts, or using the Connector/J connection property 'autoReconnect=true' to avoid this problem.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
<continued in next message>
  W 09:11:06.300 <continued from previous message>
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at com.google.apphosting.runtime.security.shared.intercept.java.lang.reflect.Constructor_.newInstance_(Constructor_.java:70)
at com.google.apphosting.runtime.security.shared.intercept.java.lang.reflect.Constructor_.newInstance(Constructor_.java:33)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1117)
at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3851)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2471)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2651)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2733)
at com.mysql.jdbc.ConnectionImpl.setAutoCommit(ConnectionImpl.java:5080)
at org.apache.commons.dbcp.DelegatingConnection.setAutoCommit(DelegatingConnection.java:371)
at org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.setAutoCommit(PoolingDataSource.java:328)
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doBegin(JdbcTransaction.java:72)
... 67 more
Caused by: java.io.IOException: Broken pipe
at java.io.RandomAccessFile.writeBytes(Native Method)
at java.io.RandomAccessFile.write(RandomAccessFile.java:502)
at com.mysql.jdbc.GoogleCloudSqlSocket$RandomAccessFileOutputStream.write(GoogleCloudSqlSocket.java:214)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3832)
... 74 more
  W 09:11:06.301 Nested in org.springframework.transaction.CannotCreateTransactionException: Could not open Hibernate Session for transaction; nested exception is org.hibernate.TransactionException: JDBC begin transaction failed: :
java.io.IOException: Broken pipe
at java.io.RandomAccessFile.writeBytes(Native Method)
at java.io.RandomAccessFile.write(RandomAccessFile.java:502)
at com.mysql.jdbc.GoogleCloudSqlSocket$RandomAccessFileOutputStream.write(GoogleCloudSqlSocket.java:214)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3832)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2471)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2651)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2733)
at com.mysql.jdbc.ConnectionImpl.setAutoCommit(ConnectionImpl.java:5080)
at org.apache.commons.dbcp.DelegatingConnection.setAutoCommit(DelegatingConnection.java:371)
at org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.setAutoCommit(PoolingDataSource.java:328)
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doBegin(JdbcTransaction.java:72)
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.begin(AbstractTransactionImpl.java:162)
at org.hibernate.internal.SessionImpl.beginTransaction(SessionImpl.java:1435)
at org.springframework.orm.hibernate4.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:474)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:373)
at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:420)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:257)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:95)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy18.loadEntityByIdNow(Unknown Source)
at com.mybusiness.web.authentication.MybusinessTokenRepository.getTokenForSeries(MybusinessTokenRepository.java:79)
at org.springframework.security.web.authentication.rememberme.PersistentTokenBasedRememberMeServices.processAutoLoginCookie(PersistentTokenBasedRememberMeServices.java:90)
at org.springframework.security.web.authentication.rememberme.AbstractRememberMeServices.autoLogin(AbstractRememberMeServices.java:115)
at org.springframework.security.web.authentication.rememberme.RememberMeAuthenticationFilter.doFilter(RememberMeAuthenticationFilter.java:97)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.ui.DefaultLoginPageGeneratingFilter.doFilter(DefaultLoginPageGeneratingFilter.java:155)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at com.google.apphosting.utils.servlet.ParseBlobUploadFilter.doFilter(ParseBlobUploadFilter.java:125)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at com.google.apphosting.runtime.jetty.SaveSessionFilter.doFilter(SaveSessionFilter.java:35)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at com.google.apphosting.utils.servlet.JdbcMySqlConnectionCleanupFilter.doFilter(JdbcMySqlConnectionCleanupFilter.java:60)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at com.google.apphosting.utils.servlet.TransactionCleanupFilter.doFilter(TransactionCleanupFilter.java:43)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
at com.google.apphosting.runtime.jetty.AppVersionHandlerMap.handle(AppVersionHandlerMap.java:254)
at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
at org.mortbay.jetty.Server.handle(Server.java:326)
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:923)
at com.google.apphosting.runtime.jetty.RpcRequestParser.parseAvailable(RpcRequestParser.java:76)
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
at com.google.apphosting.runtime.jetty.JettyServletEngineAdapter.serviceRequest(JettyServletEngineAdapter.java:146)
at com.google.apphosting.runtime.JavaRuntime$RequestRunnable.run(JavaRuntime.java:446)
at com.google.tracing.TraceContext$TraceContextRunnable.runInContext(TraceContext.java:437)
at com.google.tracing.TraceContext$TraceContextRunnable$1.run(TraceContext.java:444)
at com.google.tracing.CurrentContext.runInContext(CurrentContext.java:188)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContextNoUnref(TraceContext.java:308)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContext(TraceContext.java:300)
at com.google.tracing.TraceContext$TraceContextRunnable.run(TraceContext.java:441)
at com.google.apphosting.runtime.ThreadGroupPool$PoolEntry.run(ThreadGroupPool.java:251)
at java.lang.Thread.run(Thread.java:724)
  F 09:11:06.304 Uncaught exception from servlet
org.springframework.transaction.CannotCreateTransactionException: Could not open Hibernate Session for transaction; nested exception is org.hibernate.TransactionException: JDBC begin transaction failed: 
at org.springframework.orm.hibernate4.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:515)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:373)
at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:420)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:257)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:95)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy18.loadEntityByIdNow(Unknown Source)
at com.mybusiness.web.authentication.MybusinessTokenRepository.getTokenForSeries(MybusinessTokenRepository.java:79)
at org.springframework.security.web.authentication.rememberme.PersistentTokenBasedRememberMeServices.processAutoLoginCookie(PersistentTokenBasedRememberMeServices.java:90)
at org.springframework.security.web.authentication.rememberme.AbstractRememberMeServices.autoLogin(AbstractRememberMeServices.java:115)
at org.springframework.security.web.authentication.rememberme.RememberMeAuthenticationFilter.doFilter(RememberMeAuthenticationFilter.java:97)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.ui.DefaultLoginPageGeneratingFilter.doFilter(DefaultLoginPageGeneratingFilter.java:155)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at com.google.apphosting.utils.servlet.ParseBlobUploadFilter.doFilter(ParseBlobUploadFilter.java:125)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at com.google.apphosting.runtime.jetty.SaveSessionFilter.doFilter(SaveSessionFilter.java:35)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at com.google.apphosting.utils.servlet.JdbcMySqlConnectionCleanupFilter.doFilter(JdbcMySqlConnectionCleanupFilter.java:60)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at com.google.apphosting.utils.servlet.TransactionCleanupFilter.doFilter(TransactionCleanupFilter.java:43)
at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
at com.google.apphosting.runtime.jetty.AppVersionHandlerMap.handle(AppVersionHandlerMap.java:254)
at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
at org.mortbay.jetty.Server.handle(Server.java:326)
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:923)
at com.google.apphosting.runtime.jetty.RpcRequestParser.parseAvailable(RpcRequestParser.java:76)
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
at com.google.apphosting.runtime.jetty.JettyServletEngineAdapter.serviceRequest(JettyServletEngineAdapter.java:146)
at com.google.apphosting.runtime.JavaRuntime$RequestRunnable.run(JavaRuntime.java:446)
at com.google.tracing.TraceContext$TraceContextRunnable.runInContext(TraceContext.java:437)
at com.google.tracing.TraceContext$TraceContextRunnable$1.run(TraceContext.java:444)
at com.google.tracing.CurrentContext.runInContext(CurrentContext.java:188)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContextNoUnref(TraceContext.java:308)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContext(TraceContext.java:300)
at com.google.tracing.TraceContext$TraceContextRunnable.run(TraceContext.java:441)
at com.google.apphosting.runtime.ThreadGroupPool$PoolEntry.run(ThreadGroupPool.java:251)
at java.lang.Thread.run(Thread.java:724)
Caused by: org.hibernate.TransactionException: JDBC begin transaction failed: 
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doBegin(JdbcTransaction.java:76)
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.begin(AbstractTransactionImpl.java:162)
at org.hibernate.internal.SessionImpl.beginTransaction(SessionImpl.java:1435)
at org.springframework.orm.hibernate4.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:474)
... 64 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 38,806,609 milliseconds ago.  The last packet sent successfully to the server was 38,806,611 milliseconds ago. is longer than the server configured value of 'wait_timeout'. You should consider either expiring and/or testing connection validity before use in your application, increasing the server configured values for client timeouts, or using the Connector/J connection property 'autoReconnect=true' to avoid this problem.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingCon...(length 9816)

Answer 1

I see the following message in your stack trace:

Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 38,806,609 milliseconds ago. The last packet sent successfully to the server was 38,806,611 milliseconds ago. is longer than the server configured value of 'wait_timeout'. You should consider either expiring and/or testing connection validity before use in your application, increasing the server configured values for client timeouts, or using the Connector/J connection property 'autoReconnect=true' to avoid this problem.

If it makes sense to increase the wait timeout value, you could do it by following the instructions here .

Answer 2

I ended up following the directions here:

jdbc4 CommunicationsException

adding these two lines:

<property name="validationQuery" value="SELECT 1+1"/>
<property name="testOnBorrow" value="true" />

to my org.apache.commons.dbcp.BasicDataSource data source bean fixed this exception.