Tomcat 6 web app won't start

Question

I'm using Tomcat version 6.0.29 with JVM version 1.6.0_51-b11-456-11M4508 from Apple Inc. running on Mac OS X version 10.8.4 with x86_64 OS architecture. This is because we are using an old customer environment.

I'm using IDEA together with Ant to build the web application and the build script is running fine, except for the first time I ran the script because I then got build errors. But running the script again makes the project compile without any issues.

But the web application won't start. When trying to start it from Tomcat Web Application Manager, Tomcat says: FAIL - Application at context path /grgy could not be started and catalina.out writes:

Listening for transport dt_socket at address: 8000
2013-sep-04 20:00:40 org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: .:/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java
2013-sep-04 20:00:40 org.apache.coyote.http11.Http11Protocol init
INFO: Initializing Coyote HTTP/1.1 on http-8080
2013-sep-04 20:00:40 org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 506 ms
2013-sep-04 20:00:40 org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
2013-sep-04 20:00:40 org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/6.0.29
2013-sep-04 20:00:40 org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor host-manager.xml
2013-sep-04 20:00:41 org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor manager.xml
2013-sep-04 20:00:41 org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive jamwiki-1.2.4.war
2013-09-04 20:00:42
Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.51-b01-456 mixed mode):

"GC Daemon" daemon prio=2 tid=7fe3cfbca800 nid=0x112938000 in Object.wait() [112937000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <7654d9498> (a sun.misc.GC$LatencyLock)
    at sun.misc.GC$Daemon.run(GC.java:100)
    - locked <7654d9498> (a sun.misc.GC$LatencyLock)

"AWT-AppKit" daemon prio=5 tid=7fe3cf82f000 nid=0x7fff7667b180 runnable [00000000]
   java.lang.Thread.State: RUNNABLE

"Low Memory Detector" daemon prio=5 tid=7fe3d0019000 nid=0x111bb2000 runnable [00000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread1" daemon prio=9 tid=7fe3d0018000 nid=0x111aaf000 runnable [00000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" daemon prio=9 tid=7fe3d0017800 nid=0x1119ac000 waiting on condition [00000000]
   java.lang.Thread.State: RUNNABLE

"JDWP Event Helper Thread" daemon prio=5 tid=7fe3d0016800 nid=0x1118a9000 runnable [00000000]
   java.lang.Thread.State: RUNNABLE

"JDWP Transport Listener: dt_socket" daemon prio=5 tid=7fe3d0016000 nid=0x1117a6000 runnable [00000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" daemon prio=9 tid=7fe3cc8fe000 nid=0x11169d000 waiting on condition [00000000]
   java.lang.Thread.State: RUNNABLE

"Surrogate Locker Thread (Concurrent GC)" daemon prio=5 tid=7fe3cc8fd000 nid=0x11159a000 waiting on condition [00000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=8 tid=7fe3d0015000 nid=0x11138f000 in Object.wait() [11138e000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <765330cf8> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
    - locked <765330cf8> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
    at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:171)

"Reference Handler" daemon prio=10 tid=7fe3d0014800 nid=0x11128c000 in Object.wait() [11128b000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <765330bc0> (a java.lang.ref.Reference$Lock)
    at java.lang.Object.wait(Object.java:485)
    at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
    - locked <765330bc0> (a java.lang.ref.Reference$Lock)

"main" prio=5 tid=7fe3cd001000 nid=0x107488000 waiting on condition [107485000]
   java.lang.Thread.State: TIMED_WAITING (sleeping)
    at java.lang.Thread.sleep(Native Method)
    at sun.tools.attach.MacosxVirtualMachine.<init>(MacosxVirtualMachine.java:76)
    at sun.tools.attach.MacosxAttachProvider.attachVirtualMachine(MacosxAttachProvider.java:34)
    at com.sun.tools.attach.VirtualMachine.attach(VirtualMachine.java:195)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at net.sf.ehcache.pool.sizeof.AgentLoader.loadAgent(AgentLoader.java:131)
    at net.sf.ehcache.pool.sizeof.AgentSizeOf.<clinit>(AgentSizeOf.java:33)
    at net.sf.ehcache.pool.impl.DefaultSizeOfEngine.<init>(DefaultSizeOfEngine.java:86)
    at net.sf.ehcache.CacheManager.createSizeOfEngine(CacheManager.java:1820)
    at net.sf.ehcache.CacheManager.doInit(CacheManager.java:375)
    at net.sf.ehcache.CacheManager.init(CacheManager.java:352)
    at net.sf.ehcache.CacheManager.<init>(CacheManager.java:237)
    at org.jamwiki.utils.WikiCache.initialize(WikiCache.java:114)
    at org.jamwiki.servlets.JAMWikiListener.contextInitialized(JAMWikiListener.java:39)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4135)
    at org.apache.catalina.core.StandardContext.start(StandardContext.java:4630)
    - locked <7654fe068> (a org.apache.catalina.core.StandardContext)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:791)
    - locked <7654c5390> (a java.util.HashMap)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:771)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:546)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:905)
    at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:740)
    at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:500)
    at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1277)
    at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:321)
    at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
    - locked <7654c52f8> (a org.apache.catalina.core.StandardHost)
    at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
    - locked <7654c52f8> (a org.apache.catalina.core.StandardHost)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
    - locked <7654af570> (a org.apache.catalina.core.StandardEngine)
    at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:445)
    at org.apache.catalina.core.StandardService.start(StandardService.java:519)
    - locked <7654af570> (a org.apache.catalina.core.StandardEngine)
    at org.apache.catalina.core.StandardServer.start(StandardServer.java:710)
    - locked <7654ca930> (a [Lorg.apache.catalina.Service;)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:581)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)

"VM Thread" prio=9 tid=7fe3d0010000 nid=0x111189000 runnable 

"Gang worker#0 (Parallel GC Threads)" prio=9 tid=7fe3cc800800 nid=0x10a8cb000 runnable 

"Gang worker#1 (Parallel GC Threads)" prio=9 tid=7fe3cc801000 nid=0x10a9ce000 runnable 

"Gang worker#2 (Parallel GC Threads)" prio=9 tid=7fe3cc802000 nid=0x10aad1000 runnable 

"Gang worker#3 (Parallel GC Threads)" prio=9 tid=7fe3cc802800 nid=0x10abd4000 runnable 

"Concurrent Mark-Sweep GC Thread" prio=9 tid=7fe3cc87d800 nid=0x110e00000 runnable 
"VM Periodic Task Thread" prio=10 tid=7fe3d0022800 nid=0x111cb5000 waiting on condition 

"Exception Catcher Thread" prio=10 tid=7fe3cd001800 nid=0x1076f2000 runnable 
JNI global references: 4552

Heap
 par new generation   total 31040K, used 7757K [760000000, 7621a0000, 765330000)
  eden space 27648K,  15% used [760000000, 7604436a8, 761b00000)
  from space 3392K, 100% used [761e50000, 7621a0000, 7621a0000)
  to   space 3392K,   0% used [761b00000, 761b00000, 761e50000)
 concurrent mark-sweep generation total 240896K, used 2851K [765330000, 773e70000, 7e0000000)
 concurrent-mark-sweep perm gen total 25280K, used 25006K [7e0000000, 7e18b0000, 800000000)

2013-sep-04 20:00:48 org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory docs
2013-sep-04 20:00:48 org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory examples
2013-sep-04 20:00:48 org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory grgy
2013-sep-04 20:00:51 com.sun.xml.ws.transport.http.servlet.WSServletContextListener contextInitialized
INFO: WSSERVLET12: JAX-WS context listener initializing
2013-sep-04 20:00:54 com.sun.xml.ws.server.MonitorBase createRoot
INFO: Metro monitoring rootname successfully set to: com.sun.metro:pp=/,type=WSEndpoint,name=/grgy-ChangeDocumentStatusService-ChangeDocumentStatusPort
2013-sep-04 20:00:54 com.sun.xml.ws.transport.http.servlet.WSServletDelegate <init>
INFO: WSSERVLET14: JAX-WS servlet initializing
2013-sep-04 20:00:54 org.apache.catalina.core.StandardContext start
ALLVARLIG: Error listenerStart
2013-sep-04 20:00:54 org.apache.catalina.core.StandardContext start
ALLVARLIG: Context [/grgy] startup failed due to previous errors
2013-sep-04 20:00:54 com.sun.xml.ws.transport.http.servlet.WSServletDelegate destroy
INFO: WSSERVLET15: JAX-WS servlet destroyed
2013-sep-04 20:00:54 com.sun.xml.ws.server.MonitorBase closeMOM
INFO: Closing Metro monitoring root: com.sun.metro:pp=/,type=WSEndpoint,name=/grgy-ChangeDocumentStatusService-ChangeDocumentStatusPort
2013-sep-04 20:00:54 com.sun.xml.ws.transport.http.servlet.WSServletContextListener contextDestroyed
INFO: WSSERVLET13: JAX-WS context listener destroyed
2013-sep-04 20:00:54 org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
ALLVARLIG: The web application [/grgy] registered the JBDC driver [com.mysql.jdbc.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
2013-sep-04 20:00:54 org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
ALLVARLIG: The web application [/grgy] appears to have started a thread named [MySQL Statement Cancellation Timer] but has failed to stop it. This is very likely to create a memory leak.
2013-sep-04 20:00:54 org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
ALLVARLIG: The web application [/grgy] created a ThreadLocal with key of type [null] (value [com.sun.xml.bind.v2.runtime.Coordinator$1@5ca554da]) and a value of type [java.lang.Object[]] (value [[Ljava.lang.Object;@6a65e3ba]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
2013-sep-04 20:00:54 org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
ALLVARLIG: The web application [/grgy] created a ThreadLocal with key of type [null] (value [org.glassfish.gmbal.generic.OperationTracer$1@4749fee8]) and a value of type [java.util.ArrayList] (value [[]]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
2013-sep-04 20:00:54 org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
ALLVARLIG: The web application [/grgy] created a ThreadLocal with key of type [null] (value [com.sun.xml.bind.v2.ClassFactory$1@4afe55e8]) and a value of type [java.util.WeakHashMap] (value [{class com.sun.xml.ws.runtime.config.Tubelines=java.lang.ref.WeakReference@7b4e5966, class com.sun.xml.ws.runtime.config.TubelineDefinition=java.lang.ref.WeakReference@54cf76c8, class com.sun.xml.ws.runtime.config.MetroConfig=java.lang.ref.WeakReference@7f6ff8, class javax.xml.bind.annotation.W3CDomHandler=java.lang.ref.WeakReference@2e900309, class java.util.ArrayList=java.lang.ref.WeakReference@70b75bc0, class com.sun.xml.ws.runtime.config.TubeFactoryConfig=java.lang.ref.WeakReference@15e8d410, class com.sun.xml.ws.runtime.config.TubeFactoryList=java.lang.ref.WeakReference@68ba71ac, class javax.xml.bind.annotation.adapters.CollapsedStringAdapter=java.lang.ref.WeakReference@287d08eb}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
log4j:ERROR LogMananger.repositorySelector was null likely due to error in class reloading, using NOPLoggerRepository.
2013-sep-04 20:00:55 org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory ROOT
2013-sep-04 20:00:55 org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
2013-sep-04 20:00:55 org.apache.jk.common.ChannelSocket init
INFO: JK: ajp13 listening on /0.0.0.0:8009
2013-sep-04 20:00:55 org.apache.jk.server.JkMain start
INFO: Jk running ID=0 time=0/27  config=null
2013-sep-04 20:00:55 org.apache.catalina.startup.Catalina start
INFO: Server startup in 14515 ms

In catalina.sh I have modified the following as follows:

if [ -z "$LOGGING_MANAGER" ]; then
  JAVA_OPTS="$JAVA_OPTS -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Dfile.encoding=UTF-8 -Xms256m -Xmx2048m -XX:MaxPermSize=512m -Djava.awt.headless=true"
else 
  JAVA_OPTS="$JAVA_OPTS $LOGGING_MANAGER -Dfile.encoding=UTF-8 -Xms256m -Xmx2048m -XX:MaxPermSize=512m -Djava.awt.headless=true"
fi

Any ideas what seems to be the problem and how I should get my web app up and running again?

Kind regards, Jonas

Answer 1

Apparently things weren't that complicated after all...

I read the log from catalina.out again and noticed that a thread was waiting for JAMWikiListener. In the Tomcat Web Application Manager, JAMWiki was starting correctly but when I tried to use the app I received an ugly error message saying that the app wasn't working (of course I'm paraphrasing).

So I removed the JAMWiki app from my web app folder and from that things are working correctly again.

Regards, Jonas