Why Does My Server Stop Responding and is There A Way To Monitor It?

Question

I have a Java Web App that I am running in Tomcat 8.0. Up to this point I have had no issues with the application but the primary user has asked for several things to be on the main page of the application and I am adding these one at a time for the primary purpose of testing functionality as I go.

Here recently I have really bearing down on testing to ensure that the site is going to work properly when it is ready to deploy. After doing several tests back to back I have noticed that the server just seems to lock up. At first I thought it was memory space but I have checked all of the logs and don't seem to be getting any errors except the

29-Oct-2014 16:28:16.520 INFO [main] org.apache.catalina.core.AprLifecycleListener.init The APR 
based Apache Tomcat Native library which allows optimal performance in production environments 
was not found on the java.library.path:

The rest seemed pretty normal to me:

29-Oct-2014 16:28:16.658 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-4273"]
29-Oct-2014 16:28:16.682 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector     Using a shared selector for servlet write/read
29-Oct-2014 16:28:16.684 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["ajp-nio-8009"]
29-Oct-2014 16:28:16.686 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
29-Oct-2014 16:28:16.686 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 344 ms
29-Oct-2014 16:28:16.703 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service Catalina
29-Oct-2014 16:28:16.703 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.0.9
29-Oct-2014 16:28:16.718 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive C:\Tomcat 8.0\webapps\SecureAutoData1.war
29-Oct-2014 16:28:17.281 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive C:\Tomcat 8.0\webapps\SecureAutoData1.war has finished in 562 ms
29-Oct-2014 16:28:17.281 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\docs
29-Oct-2014 16:28:17.459 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory C:\Tomcat 8.0\webapps\docs has finished in 178 ms
29-Oct-2014 16:28:17.459 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\examples
29-Oct-2014 16:28:17.786 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory C:\Tomcat 8.0\webapps\examples has finished in 327 ms
29-Oct-2014 16:28:17.786 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\host-manager
29-Oct-2014 16:28:17.965 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory C:\Tomcat 8.0\webapps\host-manager has finished in 179 ms
29-Oct-2014 16:28:17.965 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\manager
29-Oct-2014 16:28:18.119 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory C:\Tomcat 8.0\webapps\manager has finished in 154 ms
29-Oct-2014 16:28:18.119 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\ROOT
29-Oct-2014 16:28:18.261 INFO [localhost-startStop-1]     org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory     C:\Tomcat 8.0\webapps\ROOT has finished in 142 ms
29-Oct-2014 16:28:18.262 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-4273"]
29-Oct-2014 16:28:18.267 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["ajp-nio-8009"]
29-Oct-2014 16:28:18.268 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in     1581 ms

commons-dqemon.2014-10-29:

[2014-10-29 16:11:18] [info]  [ 5144] Commons Daemon procrun (1.0.15.0 64-bit) started
[2014-10-29 16:11:18] [info]  [ 5144] Running 'Tomcat8' Service...
[2014-10-29 16:11:18] [info]  [ 3344] Starting service...
[2014-10-29 16:11:19] [info]  [ 3344] Service started in 1106 ms.
[2014-10-29 16:27:57] [info]  [ 6536] Stopping service...
[2014-10-29 16:28:02] [info]  [ 6536] Service stop thread completed.
[2014-10-29 16:28:02] [info]  [ 5144] Run service finished.
[2014-10-29 16:28:02] [info]  [ 5144] Commons Daemon procrun finished
[2014-10-29 16:28:16] [info]  [ 6532] Commons Daemon procrun (1.0.15.0 64-bit) started
[2014-10-29 16:28:16] [info]  [ 6532] Running 'Tomcat8' Service...
[2014-10-29 16:28:16] [info]  [ 7900] Starting service...
[2014-10-29 16:28:17] [info]  [ 7900] Service started in 1111 ms.

tomcat8-stdout.2014-10-29:

2014-10-29 16:11:18 Commons Daemon procrun stdout initialized
Session ID 7D825AD72EAFB71E3E22DC3FBE59D196 destroyed at Wed Oct 29 16:12:20 EDT 2014
Session ID 8F72C027CFB28678FFE8A614353BBED7 created at Wed Oct 29 16:16:47 EDT 2014
Session ID 8F70D0F8CE0EBC149412E6DC9525AC55 created at Wed Oct 29 16:27:40 EDT 2014

2014-10-29 16:28:16 Commons Daemon procrun stdout initialized
Session ID 8F72C027CFB28678FFE8A614353BBED7 destroyed at Wed Oct 29 16:34:18 EDT 2014

Until I get to the point that the server locks up and I terminate the application, then I get an error about the application still processing a request as it is terminated and the potential threat to memory leakage. that is provided in the catalina log file below:

29-Oct-2014 16:11:19.169 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-4273"]
29-Oct-2014 16:11:19.190 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
29-Oct-2014 16:11:19.192 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["ajp-nio-8009"]
29-Oct-2014 16:11:19.194 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
29-Oct-2014 16:11:19.194 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 337 ms
29-Oct-2014 16:11:19.209 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service Catalina
29-Oct-2014 16:11:19.209 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.0.9
29-Oct-2014 16:11:19.224 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive C:\Tomcat 8.0\webapps\SecureAutoData1.war
29-Oct-2014 16:11:19.788 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive C:\Tomcat 8.0\webapps\SecureAutoData1.war has finished in 563 ms
29-Oct-2014 16:11:19.788 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\docs
29-Oct-2014 16:11:19.960 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory C:\Tomcat 8.0\webapps\docs has finished in 172 ms
29-Oct-2014 16:11:19.960 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\examples
29-Oct-2014 16:11:20.303 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory C:\Tomcat 8.0\webapps\examples has finished in 343 ms
29-Oct-2014 16:11:20.303 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\host-manager
29-Oct-2014 16:11:20.472 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory C:\Tomcat 8.0\webapps\host-manager has finished in 169 ms
29-Oct-2014 16:11:20.472 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\manager
29-Oct-2014 16:11:20.633 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory C:\Tomcat 8.0\webapps\manager has finished in 161 ms
29-Oct-2014 16:11:20.634 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\ROOT
29-Oct-2014 16:11:20.790 INFO [localhost-startStop-1]     org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory     C:\Tomcat 8.0\webapps\ROOT has finished in 156 ms
29-Oct-2014 16:11:20.792 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-4273"]
29-Oct-2014 16:11:20.797 INFO [main] org.apache.coyote.AbstractProtocol.start Starting     ProtocolHandler ["ajp-nio-8009"]
29-Oct-2014 16:11:20.798 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in     1603 ms
29-Oct-2014 16:27:57.767 INFO [Thread-6] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-4273"]
29-Oct-2014 16:27:57.820 INFO [Thread-6] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-nio-8009"]
29-Oct-2014 16:27:57.870 INFO [Thread-6] org.apache.catalina.core.StandardService.stopInternal Stopping service Catalina
29-Oct-2014 16:27:57.885 INFO [localhost-startStop-2] org.apache.catalina.core.StandardWrapper.unload Waiting for 1 instance(s) to be deallocated for Servlet [LoginControl]
29-Oct-2014 16:27:58.885 INFO [localhost-startStop-2] org.apache.catalina.core.StandardWrapper.unload Waiting for 1 instance(s) to be deallocated for Servlet [LoginControl]
29-Oct-2014 16:27:59.885 INFO [localhost-startStop-2] org.apache.catalina.core.StandardWrapper.unload Waiting for 1 instance(s) to be deallocated for Servlet [LoginControl]
29-Oct-2014 16:27:59.986 INFO [localhost-startStop-2] org.apache.catalina.core.StandardWrapper.unload Waiting for 1 instance(s) to be deallocated for Servlet [DirectoryAssistance]
29-Oct-2014 16:28:00.986 INFO [localhost-startStop-2] org.apache.catalina.core.StandardWrapper.unload Waiting for 1 instance(s) to be deallocated for Servlet [DirectoryAssistance]
29-Oct-2014 16:28:01.986 INFO [localhost-startStop-2] org.apache.catalina.core.StandardWrapper.unload     Waiting for 1 instance(s) to be deallocated for Servlet [DirectoryAssistance]
29-Oct-2014 16:28:02.102 WARNING [localhost-startStop-2]     org.apache.catalina.loader.WebappClassLoader.clearReferencesThreads The web application     [/SecureAutoData1] appears to have started a thread named [Abandoned connection cleanup thread] but     has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.lang.ref.ReferenceQueue.remove(Unknown Source)
 com.mysql.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:41)
29-Oct-2014 16:28:02.103 WARNING [localhost-startStop-2]     org.apache.catalina.loader.WebappClassLoader.clearReferencesThreads The web application     [/SecureAutoData1] is still processing a request that has yet to finish. This is very likely to     create a memory leak. You can control the time allowed for requests to finish by using the     unloadDelay attribute of the standard Context implementation. Stack trace of request processing         thread:
 sun.misc.Unsafe.park(Native Method)
 java.util.concurrent.locks.LockSupport.park(Unknown Source)
 java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(Unknown Source)
 org.apache.tomcat.dbcp.pool2.impl.LinkedBlockingDeque.takeFirst(LinkedBlockingDeque.java:523)
 org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:435)
 org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:358)
 org.apache.tomcat.dbcp.dbcp2.PoolingDataSource.getConnection(PoolingDataSource.java:118)
 org.apache.tomcat.dbcp.dbcp2.BasicDataSource.getConnection(BasicDataSource.java:1412)
 com.secureautodata.business.data.DBConnector.getConnection(DBConnector.java:47)
 com.secureautodata.business.data.LeadFactory.fetchAdminLeads(LeadFactory.java:49)
 com.secureautodata.control.DirectoryAssistance.doPost(DirectoryAssistance.java:668)
 javax.servlet.http.HttpServlet.service(HttpServlet.java:644)
 javax.servlet.http.HttpServlet.service(HttpServlet.java:725)
     org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291)
 org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
         org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
 org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
 org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
 org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:503)
 org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:136)
 org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
 org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610)
 org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
 org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:526)
 org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1078)
 org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:655)
         org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:22    2)
 org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1566)
 org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1523)
 java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
 java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
 org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
 java.lang.Thread.run(Unknown Source)
29-Oct-2014 16:28:02.105 WARNING [localhost-startStop-2]     org.apache.catalina.loader.WebappClassLoader.clearReferencesThreads The web application     [/SecureAutoData1] is still processing a request that has yet to finish. This is very likely to         create a memory leak. You can control the time allowed for requests to finish by using the     unloadDelay attribute of the standard Context implementation. Stack trace of request processing     thread:
 sun.misc.Unsafe.park(Native Method)
 java.util.concurrent.locks.LockSupport.park(Unknown Source)
 java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(Unknown Source)
 org.apache.tomcat.dbcp.pool2.impl.LinkedBlockingDeque.takeFirst(LinkedBlockingDeque.java:523)
 org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:435)
 org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:358)
 org.apache.tomcat.dbcp.dbcp2.PoolingDataSource.getConnection(PoolingDataSource.java:118)
 org.apache.tomcat.dbcp.dbcp2.BasicDataSource.getConnection(BasicDataSource.java:1412)
 com.secureautodata.business.data.DBConnector.getConnection(DBConnector.java:47)
 com.secureautodata.business.data.DealerFactory.fetchDealer(DealerFactory.java:278)
 com.secureautodata.control.LoginControl.doPost(LoginControl.java:99)
 javax.servlet.http.HttpServlet.service(HttpServlet.java:644)
 javax.servlet.http.HttpServlet.service(HttpServlet.java:725)
         org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291)
 org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
         org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
 org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
 org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
 org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:503)
 org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:136)
 org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
 org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610)
 org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
 org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:526)
 org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1078)
 org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:655)
         org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:22    2)
 org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1566)
 org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1523)
 java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
 java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
 org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
 java.lang.Thread.run(Unknown Source)
29-Oct-2014 16:28:02.119 INFO [Thread-6] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-4273"]
29-Oct-2014 16:28:02.188 INFO [Thread-6] org.apache.coyote.AbstractProtocol.stop Stopping     ProtocolHandler ["ajp-nio-8009"]
29-Oct-2014 16:28:16.520 INFO [main] org.apache.catalina.core.AprLifecycleListener.init The APR based     Apache Tomcat Native library which allows optimal performance in production environments was not     found on the java.library.path: C:\Tomcat     8.0\bin;C:\Windows\Sun\Java\bin;C:\Windows\system32;C:\Windows;C:\Program Files (x86)\Intel\iCLS     Client\;C:\Program Files\Intel\iCLS     Client\;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell    \v1.0\;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files     (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management     Engine Components\IPT;C:\Program Files (x86)\Intel\Intel(R) Management Engine     Components\IPT;C:\Program Files\Java\jdk1.8.0_11\bin;C:\Program Files (x86)\MySQL\MySQL Utilities     1.3.6\;C:\Program Files\MySQL\MySQL Server     5.6\bin;C:\wamp\bin\php\php5.5.12;C:\ProgramData\ComposerSetup\bin;C:\Maven\apache-maven-    3.2.2\bin;C:\apache-ant-1.9.4-bin\apache-ant-1.9.4\bin;C:\Python27;C:\Program Files     (x86)\scala\bin;C:\Program Files (x86)\scala\bin;;.
29-Oct-2014 16:28:16.658 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-4273"]
29-Oct-2014 16:28:16.682 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
29-Oct-2014 16:28:16.684 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["ajp-nio-8009"]
29-Oct-2014 16:28:16.686 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
29-Oct-2014 16:28:16.686 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 344 ms
29-Oct-2014 16:28:16.703 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service Catalina
29-Oct-2014 16:28:16.703 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.0.9
29-Oct-2014 16:28:16.718 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive C:\Tomcat 8.0\webapps\SecureAutoData1.war
29-Oct-2014 16:28:17.281 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive C:\Tomcat 8.0\webapps\SecureAutoData1.war has finished in 562 ms
29-Oct-2014 16:28:17.281 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\docs
29-Oct-2014 16:28:17.459 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory C:\Tomcat 8.0\webapps\docs has finished in 178 ms
29-Oct-2014 16:28:17.459 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\examples
29-Oct-2014 16:28:17.786 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory C:\Tomcat 8.0\webapps\examples has finished in 327 ms
29-Oct-2014 16:28:17.786 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\host-manager
29-Oct-2014 16:28:17.965 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory C:\Tomcat 8.0\webapps\host-manager has finished in 179 ms
29-Oct-2014 16:28:17.965 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\manager
29-Oct-2014 16:28:18.119 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory C:\Tomcat 8.0\webapps\manager has finished in 154 ms
29-Oct-2014 16:28:18.119 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory C:\Tomcat 8.0\webapps\ROOT
29-Oct-2014 16:28:18.261 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory C:\Tomcat 8.0\webapps\ROOT has finished in 142 ms
29-Oct-2014 16:28:18.262 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-4273"]
29-Oct-2014 16:28:18.267 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["ajp-nio-8009"]
29-Oct-2014 16:28:18.268 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 1581 ms

The only time I see the error is when I close the web application because it will not load, I have left it for upwards of 15 minutes and came back to the computer to see the waiting on local host still sitting at the bottom of the same screen that was there when I walked away.

I apologize for including all of the information I have from all of the files in my logs but I wanted to be thorough. I noticed that it was talking about a concurrent locking error, but other than my connection pooling and whatever threads the server itself is running I don't believe there are any other threads that I have written in, or maybe that is the issue. I am not really sure, I am hoping you guys can help me. Thanks in advance!

Okay So I think That the answer is definitely a connection pool connection not being released, I was in to big of a hurry trying to finish the next part of my project and forgot to add my release and close statements in several of my data classes, however, I went back and added the release statements and then ran my project, I got this error:

Oct 29, 2014 9:40:10 PM org.apache.catalina.core.ApplicationDispatcher invoke
SEVERE: Servlet.service() for servlet jsp threw exception
java.util.ServiceConfigurationError: javax.xml.parsers.SAXParserFactory: Provider         org.apache.xerces.jaxp.SAXParserFactoryImpl not found
    at java.util.ServiceLoader.fail(Unknown Source)
    at java.util.ServiceLoader.access$300(Unknown Source)
    at java.util.ServiceLoader$LazyIterator.nextService(Unknown Source)
    at java.util.ServiceLoader$LazyIterator.next(Unknown Source)
    at java.util.ServiceLoader$1.next(Unknown Source)
    at javax.xml.parsers.FactoryFinder$1.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at javax.xml.parsers.FactoryFinder.findServiceProvider(Unknown Source)
    at javax.xml.parsers.FactoryFinder.find(Unknown Source)
    at javax.xml.parsers.SAXParserFactory.newInstance(Unknown Source)
    at org.apache.taglibs.standard.tlv.JstlBaseTLV.validate(JstlBaseTLV.java:161)
    at org.apache.taglibs.standard.tlv.JstlCoreTLV.validate(JstlCoreTLV.java:105)
    at org.apache.jasper.compiler.TagLibraryInfoImpl.validate(TagLibraryInfoImpl.java:378)
    at org.apache.jasper.compiler.Validator.validateXmlView(Validator.java:1883)
    at org.apache.jasper.compiler.Validator.validateExDirectives(Validator.java:1852)
    at org.apache.jasper.compiler.Compiler.generateJava(Compiler.java:217)
    at org.apache.jasper.compiler.Compiler.compile(Compiler.java:356)
    at org.apache.jasper.compiler.Compiler.compile(Compiler.java:336)
    at org.apache.jasper.compiler.Compiler.compile(Compiler.java:323)
    at org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:564)
    at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:357)
    at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:391)
    at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:335)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:725)
    at         org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
    at         org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:721)
    at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:466)
    at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:391)
    at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:318)
    at com.secureautodata.control.LoginControl.handler(LoginControl.java:199)
    at com.secureautodata.control.LoginControl.doPost(LoginControl.java:111)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:644)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:725)
    at         org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
    at         org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
    at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:534)
    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1081)

This smells like a database connection leak: some function is not closing a connection and therefor not returning a connection to the pool. After a while all functions using a database connection will wait (forever) for a database connection from a pool that is empty (indicated by "borrowObject" and "takeFirst" in the stack-trace). You can find some hints on how to resolve this [here](http://stackoverflow.com/a/22259478/3080094). — vanOekel, Oct 30 '14 at 00:24
@vanOekel I have to assume that you are right I was in to big of a hurry to get an iteration done and completely overlooked the releasing and closing of statements and result sets, There are some edits to my question though, I got a new error that I am not sure where to start, any ideas? — , Oct 30 '14 at 01:59
Have you tried any of the answers [here](http://stackoverflow.com/q/1016286/3080094)? — vanOekel, Oct 30 '14 at 18:14
@vanOekel I am about to post the answer to this question, and you should get the credit for it absolutely without a doubt. The locking issue was my anxiousness to get an iteration in under my deadline and not properly or effectively freeing up a connection when it was done being used in the build class for my schedule, how I forgot this detail is beyond me because I was so strategic to do it in all of my other build classes.This was also most likely the issue with my pagination because it presented the same issues. The other issue I found was a conflicting dependency in maven. — , Oct 30 '14 at 23:04
No problem, it's good to see you took the time to write a complete answer to your question. And you can always upvote any answers/question (that I linked to in my comments) that helped you. — vanOekel, Oct 31 '14 at 00:29

score 2 · Answer 1 · answered Oct 30 '14 at 23:17

Okay so the answer to this question was under my nose the whole time. @vanOekel presented to me that it could be a Connection pool issue where the connections were not being released. In my haste trying to tie up part of my project I had completely overlooked the closing of open connections in one of my classes.

After resolving that issue I ran into an error where my pom.xml file presented a dependency that was in conflict with a couple of .jar files that I had added to my library. The main one was the mysql connector jar, I had reinstalled tomcat on my computer at work and as a quick work around instead of including the jar in my tomcat library I just added it to my pom.xml as a dependency causing a conflict with my tomcat and IDE setup on my home computer.

After removing this dependency from the pom.xml and my jstl dependency from my pom.xml everything worked like a dream.

I have tested with several runs through and found that it no longer locks up. It seems that the connections are being released as they are supposed to be and that the site is now running properly.

score 1 · Answer 2 · answered Jan 04 '16 at 17:56

This may come in useful to some of you looking for similar answers but are running other JDBC drivers:

I've found the postgres driver to be particularly unfriendly, not only does it not deregister itself but it also starts some sort of timer thread that does not stop or respond to an interrupt() request so even manually deregistering doesn't work straight off and prevents a clean shutdown of tomcat.

The following code added to a contextDestroyed method of a ServletContextListener helps a lot with a clean(-ish) shutdown. I had to call stop() on the errant thread but I can't see any other way of killing it.

@Override
public void contextDestroyed(ServletContextEvent sce) {
    killUnstoppableThreads();
    unregisterJdbcDrivers();
}

private void unregisterJdbcDrivers() {
    Enumeration<Driver> drivers = DriverManager.getDrivers();
    Driver d = null;
    while (drivers.hasMoreElements()) {
        try {
            d = drivers.nextElement();
            DriverManager.deregisterDriver(d);
            logger.error(String.format("Driver %s deregistered", d));

        } catch (SQLException ex) {
            logger.error(String.format("Error deregistering driver %s", d), ex);
        }
    }

}

private void killUnstoppableThreads() {
    ThreadMXBean threadMxBean = ManagementFactory.getThreadMXBean();
    ThreadInfo[] threadInfo = threadMxBean.dumpAllThreads(true, true);

    String threadName = "PostgreSQL-JDBC-SharedTimer-";
    long id = -1;
    for (ThreadInfo info : threadInfo) {
        if (info.getThreadName() != null && info.getThreadName().startsWith(threadName)) {
            id = info.getThreadId();
            for (Thread t : Thread.getAllStackTraces().keySet()) {
                if (t.getId() == id) {
                    logger.info("Killing " + info.getThreadName() + " thread");
                    t.stop(); // thread doesn't respond to interrupt()!
                    break;
                }
            }
        }
    }
}

score 0 · Answer 3 · answered Oct 30 '14 at 22:20

Take a thread dump and see if there are any threads containing application code in WAIT state in case you are looking for a concurrency bottleneck. On *nix you can get a thread dump by sending

kill -3

Under Windows you can send to the application's window. The thread dump goes to stdout.

Hope this helps.

Slava

score -1 · Answer 4 · answered Oct 29 '14 at 21:14

The easiest way you can monitor what is going on inside the java process on Windows machine is by using jconsole tool provided with jdk.

There is a tutorial how to use it on Oracle website: http://docs.oracle.com/javase/7/docs/technotes/guides/management/jconsole.html

Why Does My Server Stop Responding and is There A Way To Monitor It?

4 Answers4