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ElasticSearch 5.2.2 socket read timed out

I moved from 2.2 to 5.2.2 of ES. I've been running some tests and have been getting two errors (one from logger and one from ES)
Logger:
java.net.SocketTimeoutException: Read timed out
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.socketRead(SocketInputStream.java:116)
at java.net.SocketInputStream.read(SocketInputStream.java:170)
at java.net.SocketInputStream.read(SocketInputStream.java:141)
at org.apache.http.impl.io.SessionInputBufferImpl.streamRead(SessionInputBufferImpl.java:136)
at org.apache.http.impl.io.SessionInputBufferImpl.fillBuffer(SessionInputBufferImpl.java:152)
at org.apache.http.impl.io.SessionInputBufferImpl.readLine(SessionInputBufferImpl.java:270)
at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:140)
at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:57)
at org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:260)
at org.apache.http.impl.DefaultBHttpClientConnection.receiveResponseHeader(DefaultBHttpClientConnection.java:161)
at sun.reflect.GeneratedMethodAccessor832.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.http.impl.conn.CPoolProxy.invoke(CPoolProxy.java:138)
at com.sun.proxy.$Proxy325.receiveResponseHeader(Unknown Source)
at org.apache.http.protocol.HttpRequestExecutor.doReceiveResponse(HttpRequestExecutor.java:271)
at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:123)
at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:254)
at org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:195)
at org.apache.http.impl.execchain.RetryExec.execute(RetryExec.java:86)
at org.apache.http.impl.execchain.RedirectExec.execute(RedirectExec.java:108)
at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:186)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
at io.searchbox.client.http.JestHttpClient.executeRequest(JestHttpClient.java:109)
at io.searchbox.client.http.JestHttpClient.execute(JestHttpClient.java:56)
at gov.nasa.jpl.view_repo.db.ElasticHelper.indexCommit(ElasticHelper.java:301)
at gov.nasa.jpl.view_repo.util.EmsNodeUtil.insertCommitIntoElastic(EmsNodeUtil.java:801)
at gov.nasa.jpl.view_repo.webscripts.ModelPost.executeImplImpl(ModelPost.java:145)
at gov.nasa.jpl.view_repo.webscripts.ModelPost.executeImpl(ModelPost.java:80)
at gov.nasa.jpl.view_repo.webscripts.DeclarativeJavaWebScript.execute(DeclarativeJavaWebScript.java:105)
at org.alfresco.repo.web.scripts.RepositoryContainer$3.execute(RepositoryContainer.java:489)
at org.alfresco.repo.transaction.RetryingTransactionHelper.doInTransaction(RetryingTransactionHelper.java:454)
at org.alfresco.repo.web.scripts.RepositoryContainer.transactionedExecute(RepositoryContainer.java:551)
at org.alfresco.repo.web.scripts.RepositoryContainer.transactionedExecuteAs(RepositoryContainer.java:619)
at org.alfresco.repo.web.scripts.RepositoryContainer.executeScriptInternal(RepositoryContainer.java:399)
at org.alfresco.repo.web.scripts.RepositoryContainer.executeScript(RepositoryContainer.java:280)
at org.springframework.extensions.webscripts.AbstractRuntime.executeScript(AbstractRuntime.java:378)
at org.springframework.extensions.webscripts.AbstractRuntime.executeScript(AbstractRuntime.java:209)
at org.springframework.extensions.webscripts.servlet.WebScriptServlet.service(WebScriptServlet.java:132)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.alfresco.web.app.servlet.GlobalLocalizationFilter.doFilter(GlobalLocalizationFilter.java:61)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
ES (I think this is unrelated to the first error, but still):
[WARN ][o.e.m.j.JvmGcMonitorService] [PnpfiI6] [gc][9162] overhead, spent [1.1s] collecting in the last [1.6s]
Jest is properly set up as a singleton called once as such:
factory.setHttpClientConfig(new HttpClientConfig.Builder(elasticHost).defaultSchemeForDiscoveredNodes("https").multiThreaded(true)
.readTimeout(180000).build());
I tried toggling the settings, turning multiThreaded on and off, adding and upping readTimeout and even connTimeout (though for production it seems like a mistake to do this).
I have especially large document that I think might be causing the timeout, but we aren't having this issue in 2.2. It's similar to a open issue on
Jest's github:
https://github.com/searchbox-io/Jest/issues/396
Any ideas on how to resolve this? And why this error does not appear on 2.2?

500 internal server error with GWT Tomcat Apache

I am getting the following error on tomcat apache server running a GWT web application. 500 internal server error the call failed on the server; see server log for details
The server log contains:
Jul 22, 2015 8:05:51 AM org.apache.catalina.core.ApplicationContext log
SEVERE: Exception while dispatching incoming RPC call
org.hibernate.AssertionFailure: null id in com.simulconsult.test.shared.model.Script entry (don't flush the Session after an exception occurs)
at org.hibernate.event.def.DefaultFlushEntityEventListener.checkId(DefaultFlushEntityEventListener.java:82)
at org.hibernate.event.def.DefaultFlushEntityEventListener.getValues(DefaultFlushEntityEventListener.java:190)
at org.hibernate.event.def.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:147)
at org.hibernate.event.def.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:219)
at org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:99)
at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1216)
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.hibernate.context.ThreadLocalSessionContext$TransactionProtectionWrapper.invoke(ThreadLocalSessionContext.java:345)
at com.sun.proxy.$Proxy61.flush(Unknown Source)
at net.sf.gilead.core.hibernate.HibernateUtil.flushIfNeeded(HibernateUtil.java:979)
at net.sf.gilead.core.PersistentBeanManager.clone(PersistentBeanManager.java:227)
at net.sf.gilead.gwt.GileadRPCHelper.parseReturnValue(GileadRPCHelper.java:157)
at net.sf.gilead.gwt.PersistentRemoteService.processCall(PersistentRemoteService.java:203)
at com.simulconsult.test.server.HibernateBasedService.processCall(HibernateBasedService.java:68)
at com.google.gwt.user.server.rpc.RemoteServiceServlet.processPost(RemoteServiceServlet.java:305)
at com.google.gwt.user.server.rpc.AbstractRemoteServiceServlet.doPost(AbstractRemoteServiceServlet.java:62)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:409)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1044)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:313)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
The same code and deployment works without error on my local tomcat apache server, but not on that of my web host provider.
Thoughts?

Apparently the error logged is related to my Script object but is not the real problem. The issue was we neglected to update the database table schema at our web host provider site.

Tomcat: Application errors when multiple WARs deployed

I am seeing something very strange after my Tomcat starts up. I have 15 applications deployed, and everything seems OK until I try to access a specific page on a specific application. There are some cross-dependencies such as services.
If I deploy the troubled application by itself, I can view the page without issue. If I deploy all the other applications one by one, I can view the page without issue. If all applications are deployed together at startup, this is when I see the following error:
SEVERE: Can't instantiate page using constructor public com.company.web.view.purchase.buy.BuyAGiftPage(org.apache.wicket.PageParameters) and argument
org.apache.wicket.WicketRuntimeException: Can't instantiate page using constructor public com.company.web.view.purchase.buy.BuyAGiftPage(org.apache.wicket.PageParameters) and argument
at org.apache.wicket.session.DefaultPageFactory.createPage(DefaultPageFactory.java:212)
at org.apache.wicket.session.DefaultPageFactory.newPage(DefaultPageFactory.java:65)
at org.apache.wicket.request.target.component.BookmarkablePageRequestTarget.newPage(BookmarkablePageRequestTarget.java:298)
at org.apache.wicket.request.target.component.BookmarkablePageRequestTarget.getPage(BookmarkablePageRequestTarget.java:320)
at org.apache.wicket.request.target.component.BookmarkablePageRequestTarget.processEvents(BookmarkablePageRequestTarget.java:234)
at org.apache.wicket.request.AbstractRequestCycleProcessor.processEvents(AbstractRequestCycleProcessor.java:92)
at org.apache.wicket.RequestCycle.processEventsAndRespond(RequestCycle.java:1252)
at org.apache.wicket.RequestCycle.step(RequestCycle.java:1331)
at org.apache.wicket.RequestCycle.steps(RequestCycle.java:1438)
at org.apache.wicket.RequestCycle.request(RequestCycle.java:546)
at org.apache.wicket.protocol.http.WicketFilter.doGet(WicketFilter.java:486)
at org.apache.wicket.protocol.http.WicketFilter.doFilter(WicketFilter.java:319)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at com.ideasx.stats.HttpFilterStatCounter.doFilter(HttpFilterStatCounter.java:87)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:409)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1044)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:313)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
at java.lang.Thread.run(Thread.java:695)
Caused by: java.lang.reflect.InvocationTargetException
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 org.apache.wicket.session.DefaultPageFactory.createPage(DefaultPageFactory.java:188)
... 30 more
Caused by: java.lang.NoClassDefFoundError: Could not initialize class net.sf.cglib.proxy.Enhancer
at org.apache.wicket.proxy.LazyInitProxyFactory.createProxy(LazyInitProxyFactory.java:159)
at org.apache.wicket.spring.injection.annot.AnnotProxyFieldValueFactory.getFieldValue(AnnotProxyFieldValueFactory.java:130)
at org.apache.wicket.injection.Injector.inject(Injector.java:103)
at org.apache.wicket.injection.ConfigurableInjector.inject(ConfigurableInjector.java:39)
at org.apache.wicket.injection.ComponentInjector.onInstantiation(ComponentInjector.java:52)
at org.apache.wicket.Application.notifyComponentInstantiationListeners(Application.java:1093)
at org.apache.wicket.Component.(Component.java:926)
at org.apache.wicket.MarkupContainer.(MarkupContainer.java:113)
at org.apache.wicket.markup.html.WebMarkupContainer.(WebMarkupContainer.java:49)
at org.apache.wicket.markup.html.WebMarkupContainerWithAssociatedMarkup.(WebMarkupContainerWithAssociatedMarkup.java:51)
at org.apache.wicket.markup.html.WebMarkupContainerWithAssociatedMarkup.(WebMarkupContainerWithAssociatedMarkup.java:43)
at org.apache.wicket.markup.html.panel.Panel.(Panel.java:76)
at com.company.web.view.purchase.buy.BuyAGiftPanel.(BuyAGiftPanel.java:54)
at com.company.web.view.purchase.buy.BuyAGiftPage.(BuyAGiftPage.java:22)
... 35 more
I have checked for dependency collisions and didn't find anything out of the ordinary. So my question is this. Given that I can deploy the applications in a specific order and not see the error, is it possible that Tomcat is responsible for this? How would I go about finding the problem?
Edited to add:
It seems that on startup, a clean session and the first request to the application throws the following cast exception:
SEVERE: Can't instantiate page using constructor public com.company.web.view.purchase.buy.BuyAGiftPage(org.apache.wicket.PageParameters) and argument
org.apache.wicket.WicketRuntimeException: Can't instantiate page using constructor public com.company.web.view.purchase.buy.BuyAGiftPage(org.apache.wicket.PageParameters) and argument
at org.apache.wicket.session.DefaultPageFactory.createPage(DefaultPageFactory.java:212)
at org.apache.wicket.session.DefaultPageFactory.newPage(DefaultPageFactory.java:65)
at org.apache.wicket.request.target.component.BookmarkablePageRequestTarget.newPage(BookmarkablePageRequestTarget.java:298)
at org.apache.wicket.request.target.component.BookmarkablePageRequestTarget.getPage(BookmarkablePageRequestTarget.java:320)
at org.apache.wicket.request.target.component.BookmarkablePageRequestTarget.processEvents(BookmarkablePageRequestTarget.java:234)
at org.apache.wicket.request.AbstractRequestCycleProcessor.processEvents(AbstractRequestCycleProcessor.java:92)
at org.apache.wicket.RequestCycle.processEventsAndRespond(RequestCycle.java:1252)
at org.apache.wicket.RequestCycle.step(RequestCycle.java:1331)
at org.apache.wicket.RequestCycle.steps(RequestCycle.java:1438)
at org.apache.wicket.RequestCycle.request(RequestCycle.java:546)
at org.apache.wicket.protocol.http.WicketFilter.doGet(WicketFilter.java:486)
at org.apache.wicket.protocol.http.WicketFilter.doFilter(WicketFilter.java:319)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at com.ideasx.stats.HttpFilterStatCounter.doFilter(HttpFilterStatCounter.java:87)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:409)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1044)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:315)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
at java.lang.Thread.run(Thread.java:695)
Caused by: java.lang.reflect.InvocationTargetException
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 org.apache.wicket.session.DefaultPageFactory.createPage(DefaultPageFactory.java:188)
... 30 more
Caused by: java.lang.ExceptionInInitializerError
at org.apache.wicket.proxy.LazyInitProxyFactory.createProxy(LazyInitProxyFactory.java:159)
at org.apache.wicket.spring.injection.annot.AnnotProxyFieldValueFactory.getFieldValue(AnnotProxyFieldValueFactory.java:130)
at org.apache.wicket.injection.Injector.inject(Injector.java:103)
at org.apache.wicket.injection.ConfigurableInjector.inject(ConfigurableInjector.java:39)
at org.apache.wicket.injection.ComponentInjector.onInstantiation(ComponentInjector.java:52)
at org.apache.wicket.Application.notifyComponentInstantiationListeners(Application.java:1093)
at org.apache.wicket.Component.(Component.java:926)
at org.apache.wicket.MarkupContainer.(MarkupContainer.java:113)
at org.apache.wicket.markup.html.WebMarkupContainer.(WebMarkupContainer.java:49)
at org.apache.wicket.markup.html.WebMarkupContainerWithAssociatedMarkup.(WebMarkupContainerWithAssociatedMarkup.java:51)
at org.apache.wicket.markup.html.WebMarkupContainerWithAssociatedMarkup.(WebMarkupContainerWithAssociatedMarkup.java:43)
at org.apache.wicket.markup.html.panel.Panel.(Panel.java:76)
at com.company.web.view.purchase.buy.BuyAGiftPanel.(BuyAGiftPanel.java:54)
at com.company.web.view.purchase.buy.BuyAGiftPage.(BuyAGiftPage.java:22)
... 35 more
Caused by: java.lang.ClassCastException: net.sf.cglib.proxy.Enhancer$EnhancerKey$$KeyFactoryByCGLIB$$7fb24d72 cannot be cast to net.sf.cglib.core.KeyFactory
at net.sf.cglib.core.KeyFactory$Generator.create(KeyFactory.java:145)
at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:117)
at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:108)
at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:104)
at net.sf.cglib.proxy.Enhancer.(Enhancer.java:69)
... 49 more

This isn't specific to Tomcat it seems. After searching some more I found that cglib_nodep dependency has some class loading issues. I excluded this library from the tree, explicitly defined cglib version 2.2 and it cleared things up.
http://forum.spring.io/forum/spring-projects/web/flex/65337-an-strange-error-with-net-sf-cglib-core-keyfactory

Remove all the server logs, all the temporary files in Tomcat and retry. This many times fix this kind of issues.

org.hibernate.exception.JDBCConnectionException: Cannot open connection

Every now and then I get the following exception. I do not get it everytime, it happens like 5 out of 10 time I request some page. I have built site using JSF + Hibernate and is deployed on Apache Tomcat.
org.hibernate.exception.JDBCConnectionException: Cannot open connection
at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:74)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:29)
at org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:426)
at org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:144)
at org.hibernate.jdbc.JDBCContext.connection(JDBCContext.java:119)
at org.hibernate.transaction.JDBCTransaction.begin(JDBCTransaction.java:57)
at org.hibernate.impl.SessionImpl.beginTransaction(SessionImpl.java:1326)
at com.bean.PostsBean.getCategoriesList(PostsBean.java:137)
at sun.reflect.GeneratedMethodAccessor291.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at javax.el.BeanELResolver.invoke(BeanELResolver.java:484)
at javax.el.CompositeELResolver.invoke(CompositeELResolver.java:161)
at org.apache.el.parser.AstValue.getValue(AstValue.java:173)
at org.apache.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:185)
at com.sun.faces.facelets.el.TagValueExpression.getValue(TagValueExpression.java:109)
at com.sun.faces.facelets.tag.jstl.core.ForEachHandler.apply(ForEachHandler.java:161)
at javax.faces.view.facelets.CompositeFaceletHandler.apply(CompositeFaceletHandler.java:95)
at com.sun.faces.facelets.compiler.NamespaceHandler.apply(NamespaceHandler.java:93)
at com.sun.faces.facelets.compiler.EncodingHandler.apply(EncodingHandler.java:87)
at com.sun.faces.facelets.impl.DefaultFacelet.include(DefaultFacelet.java:312)
at com.sun.faces.facelets.impl.DefaultFacelet.include(DefaultFacelet.java:371)
at com.sun.faces.facelets.impl.DefaultFacelet.include(DefaultFacelet.java:350)
at com.sun.faces.facelets.impl.DefaultFaceletContext.includeFacelet(DefaultFaceletContext.java:199)
at com.sun.faces.facelets.tag.ui.IncludeHandler.apply(IncludeHandler.java:120)
at javax.faces.view.facelets.CompositeFaceletHandler.apply(CompositeFaceletHandler.java:95)
at javax.faces.view.facelets.DelegatingMetaTagHandler.applyNextHandler(DelegatingMetaTagHandler.java:137)
at com.sun.faces.facelets.tag.jsf.ComponentTagHandlerDelegateImpl.apply(ComponentTagHandlerDelegateImpl.java:190)
at javax.faces.view.facelets.DelegatingMetaTagHandler.apply(DelegatingMetaTagHandler.java:120)
at javax.faces.view.facelets.CompositeFaceletHandler.apply(CompositeFaceletHandler.java:95)
at com.sun.faces.facelets.compiler.NamespaceHandler.apply(NamespaceHandler.java:93)
at com.sun.faces.facelets.compiler.EncodingHandler.apply(EncodingHandler.java:87)
at com.sun.faces.facelets.impl.DefaultFacelet.apply(DefaultFacelet.java:161)
at com.sun.faces.application.view.FaceletViewHandlingStrategy.buildView(FaceletViewHandlingStrategy.java:972)
at com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:99)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:219)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:647)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:203)
at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:181)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at com.googlecode.psiprobe.Tomcat70AgentValve.invoke(Tomcat70AgentValve.java:38)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1023)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589)
at org.apache.tomcat.util.net.AprEndpoint$SocketWithOptionsProcessor.run(AprEndpoint.java:1810)
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: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
The last packet successfully received from the server was 291,242 milliseconds ago. The last packet sent successfully to the server was 1 milliseconds ago.
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:411)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1117)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3603)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3492)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4043)
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:2788)
at com.mysql.jdbc.ConnectionImpl.setAutoCommit(ConnectionImpl.java:5282)
at com.mchange.v2.c3p0.impl.NewProxyConnection.setAutoCommit(NewProxyConnection.java:881)
at org.hibernate.connection.C3P0ConnectionProvider.getConnection(C3P0ConnectionProvider.java:61)
at org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:423)
... 55 more
Caused by: java.io.EOFException: Can not read response from server. Expected to read 4 bytes, read 0 bytes before connection was unexpectedly lost.
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:3052)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3503)
... 64 more

The message of the root exception is telling you the problem:
Caused by: java.io.EOFException: Can not read response from server. Expected to read 4 bytes, read 0 bytes before connection was unexpectedly lost.
The network connection between your server and the database server is unstable. So this is not a problem of your software.

Java Servlet and JDBC for SQL Server database

I have created the JDBCSQl.java, which is basically get one value from database. As standalone it is working fine.
When I call this class within another Servlet Java programming, null value is getting returned.
I've checked the trace log of database, it is not querying a statement at all.
I am getting the error below, when i execute. Both JDBCSQl.java and Servlet.java exists in in a single package of project.
java.lang.ClassNotFoundException: com.microsoft.sqlserver.jdbc.SQLServerDriver
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1714)
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1559)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Unknown Source)
at ValCred.UserIDandPasswordCheck.dbConnect(UserIDandPasswordCheck.java:27)
at ValCred.CredCheck.doGet(CredCheck.java:31)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1023)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:312)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
null
Thanks
Siddu

Add sql server jdbc jar in your web apps lib folder and then try.