[Eagle-i-admins] Upgrade problems 2.0MS2.17 to 2.0MS3.0.8

Norman, Neil neil.norman at vanderbilt.edu
Wed Aug 13 15:25:14 EDT 2014 

I'm trying to upgrade our test environment and running into problems with the sweet.war when I start the tomcat6 service.  After the upgrade the site will not load, and jstack shows the following.
2014-08-13 14:15:54
Full thread dump OpenJDK 64-Bit Server VM (23.25-b01 mixed mode):

"Attach Listener" daemon prio=10 tid=0x00007f7710001000 nid=0x5bfd runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"http-8443-4" daemon prio=10 tid=0x00007f76f8006800 nid=0x3dba in Object.wait() [0x00007f77142c0000]
   java.lang.Thread.State: WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        - waiting on <0x00000000fe51acc8> (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
        at java.lang.Object.wait(Object.java:502)
        at org.apache.tomcat.util.net.JIoEndpoint$Worker.await(JIoEndpoint.java:458)
        - locked <0x00000000fe51acc8> (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
        at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:484)
        at java.lang.Thread.run(Thread.java:701)

"http-8443-3" daemon prio=10 tid=0x00007f76f8004800 nid=0x3db9 in Object.wait() [0x00007f77143c1000]
   java.lang.Thread.State: WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        - waiting on <0x00000000fe51cb78> (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
        at java.lang.Object.wait(Object.java:502)
        at org.apache.tomcat.util.net.JIoEndpoint$Worker.await(JIoEndpoint.java:458)
        - locked <0x00000000fe51cb78> (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
        at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:484)
        at java.lang.Thread.run(Thread.java:701)

"http-8443-2" daemon prio=10 tid=0x00007f76f8003000 nid=0x3db8 in Object.wait() [0x00007f77144c2000]
   java.lang.Thread.State: WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        - waiting on <0x00000000fe532eb8> (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
        at java.lang.Object.wait(Object.java:502)
        at org.apache.tomcat.util.net.JIoEndpoint$Worker.await(JIoEndpoint.java:458)
        - locked <0x00000000fe532eb8> (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
        at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:484)
        at java.lang.Thread.run(Thread.java:701)

"http-8443-1" daemon prio=10 tid=0x00007f76f8001800 nid=0x3db7 in Object.wait() [0x00007f77145c3000]
   java.lang.Thread.State: WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        - waiting on <0x00000000fe533aa8> (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
        at java.lang.Object.wait(Object.java:502)
        at org.apache.tomcat.util.net.JIoEndpoint$Worker.await(JIoEndpoint.java:458)
        - locked <0x00000000fe533aa8> (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
        at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:484)
        at java.lang.Thread.run(Thread.java:701)

"http-8443-Acceptor-0" daemon prio=10 tid=0x00007f7738c5a800 nid=0x3db6 runnable [0x00007f77146c4000]
   java.lang.Thread.State: RUNNABLE
        at java.net.PlainSocketImpl.socketAccept(Native Method)
        at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:375)
        at java.net.ServerSocket.implAccept(ServerSocket.java:478)
        at sun.security.ssl.SSLServerSocketImpl.accept(SSLServerSocketImpl.java:278)
        at org.apache.tomcat.util.net.jsse.JSSESocketFactory.acceptSocket(JSSESocketFactory.java:152)
        at org.apache.tomcat.util.net.JIoEndpoint$Acceptor.run(JIoEndpoint.java:352)
        at java.lang.Thread.run(Thread.java:701)

"http-8080-Acceptor-0" daemon prio=10 tid=0x00007f77388a6000 nid=0x3db5 runnable [0x00007f7715987000]
   java.lang.Thread.State: RUNNABLE
        at java.net.PlainSocketImpl.socketAccept(Native Method)
        at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:375)
        at java.net.ServerSocket.implAccept(ServerSocket.java:478)
        at java.net.ServerSocket.accept(ServerSocket.java:446)
        at org.apache.tomcat.util.net.DefaultServerSocketFactory.acceptSocket(DefaultServerSocketFactory.java:61)
        at org.apache.tomcat.util.net.JIoEndpoint$Acceptor.run(JIoEndpoint.java:352)
        at java.lang.Thread.run(Thread.java:701)

"ContainerBackgroundProcessor[StandardEngine[Catalina]]" daemon prio=10 tid=0x00007f77383f2800 nid=0x3db4 waiting on condition [0x00007f7715a88000]
   java.lang.Thread.State: TIMED_WAITING (sleeping)
        at java.lang.Thread.sleep(Native Method)
        at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1579)
        at java.lang.Thread.run(Thread.java:701)

"SessionReaper" daemon prio=10 tid=0x00007f7738d6f800 nid=0x3db3 in Object.wait() [0x00007f77147c5000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        - waiting on <0x00000000c61e6c48> (a java.util.TaskQueue)
        at java.util.TimerThread.mainLoop(Timer.java:531)
        - locked <0x00000000c61e6c48> (a java.util.TaskQueue)
        at java.util.TimerThread.run(Timer.java:484)

"pool-1-thread-1" prio=10 tid=0x00007f7738d1f800 nid=0x3db2 waiting on condition [0x00007f77157c0000]
   java.lang.Thread.State: WAITING (parking)
        at sun.misc.Unsafe.park(Native Method)
        - parking to wait for  <0x00000000c613c0a0> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
        at java.util.concurrent.locks.LockSupport.park(LockSupport.java:186)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2043)
        at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:386)
        at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1069)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1131)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:701)

"derby.rawStoreDaemon" daemon prio=10 tid=0x00007f773882b800 nid=0x3d7e in Object.wait() [0x00007f7715d91000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        - waiting on <0x00000000c0b79370> (a org.apache.derby.impl.services.daemon.BasicDaemon)
        at org.apache.derby.impl.services.daemon.BasicDaemon.rest(Unknown Source)
        - locked <0x00000000c0b79370> (a org.apache.derby.impl.services.daemon.BasicDaemon)
        at org.apache.derby.impl.services.daemon.BasicDaemon.run(Unknown Source)
        at java.lang.Thread.run(Thread.java:701)

"Timer-0" daemon prio=10 tid=0x00007f7738849000 nid=0x3d7d in Object.wait() [0x00007f7715e92000]
   java.lang.Thread.State: WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        - waiting on <0x00000000c0b601c0> (a java.util.TaskQueue)
        at java.lang.Object.wait(Object.java:502)
        at java.util.TimerThread.mainLoop(Timer.java:505)
        - locked <0x00000000c0b601c0> (a java.util.TaskQueue)
        at java.util.TimerThread.run(Timer.java:484)

"derby.antiGC" daemon prio=10 tid=0x00007f7738749800 nid=0x3d7c in Object.wait() [0x00007f7715f93000]
   java.lang.Thread.State: WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        - waiting on <0x00000000c01c5600> (a org.apache.derby.impl.services.monitor.AntiGC)
        at java.lang.Object.wait(Object.java:502)
        at org.apache.derby.impl.services.monitor.AntiGC.run(Unknown Source)
        - locked <0x00000000c01c5600> (a org.apache.derby.impl.services.monitor.AntiGC)
        at java.lang.Thread.run(Thread.java:701)

"GC Daemon" daemon prio=10 tid=0x00007f77385ab800 nid=0x3d75 in Object.wait() [0x00007f77303bd000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        - waiting on <0x00000000c0010798> (a sun.misc.GC$LatencyLock)
        at sun.misc.GC$Daemon.run(GC.java:117)
        - locked <0x00000000c0010798> (a sun.misc.GC$LatencyLock)

"Low Memory Detector" daemon prio=10 tid=0x00007f77380f6800 nid=0x3d73 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread1" daemon prio=10 tid=0x00007f77380f4000 nid=0x3d72 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" daemon prio=10 tid=0x00007f77380f1000 nid=0x3d71 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" daemon prio=10 tid=0x00007f77380ef000 nid=0x3d70 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=10 tid=0x00007f77380a0000 nid=0x3d6f in Object.wait() [0x00007f77310e9000]
   java.lang.Thread.State: WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        - waiting on <0x00000000c00109e0> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:133)
        - locked <0x00000000c00109e0> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:149)
        at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:189)

"Reference Handler" daemon prio=10 tid=0x00007f773809d800 nid=0x3d6e in Object.wait() [0x00007f77311ea000]
   java.lang.Thread.State: WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        - waiting on <0x00000000c0010778> (a java.lang.ref.Reference$Lock)
        at java.lang.Object.wait(Object.java:502)
        at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:133)
        - locked <0x00000000c0010778> (a java.lang.ref.Reference$Lock)

"main" prio=10 tid=0x00007f7738009000 nid=0x3d69 runnable [0x00007f773f59e000]
   java.lang.Thread.State: RUNNABLE
        at java.net.PlainSocketImpl.socketAccept(Native Method)
        at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:375)
        at java.net.ServerSocket.implAccept(ServerSocket.java:478)
        at java.net.ServerSocket.accept(ServerSocket.java:446)
        at org.apache.catalina.core.StandardServer.await(StandardServer.java:389)
        at org.apache.catalina.startup.Catalina.await(Catalina.java:657)
        at org.apache.catalina.startup.Catalina.start(Catalina.java:617)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:622)
        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)

"VM Thread" prio=10 tid=0x00007f773808f000 nid=0x3d6d runnable

"GC task thread#0 (ParallelGC)" prio=10 tid=0x00007f7738016800 nid=0x3d6a runnable

"GC task thread#1 (ParallelGC)" prio=10 tid=0x00007f7738018800 nid=0x3d6b runnable

"VM Periodic Task Thread" prio=10 tid=0x00007f7738101000 nid=0x3d74 waiting on condition

JNI global references: 461


Further the catalina log is complaining about version compatibility with sweet.  I have tried a couple of different versions with no luck.

Aug 13, 2014 1:20:51 PM org.apache.catalina.startup.HostConfig deployWAR
SEVERE: Error deploying web application archive ROOT.war
java.lang.UnsupportedClassVersionError: org/eaglei/repository/servlet/RepositoryContextListener : Unsupported major.minor version 51.0 (unable to load class org.eaglei.repository.servlet.RepositoryContextListener)
        at org.apache.catalina.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:2334)
        at org.apache.catalina.loader.WebappClassLoader.findClass(WebappClassLoader.java:976)
        at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1450)
        at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1329)
        at org.apache.catalina.startup.WebAnnotationSet.loadClassAnnotation(WebAnnotationSet.java:145)
        at org.apache.catalina.startup.WebAnnotationSet.loadApplicationListenerAnnotations(WebAnnotationSet.java:73)
        at org.apache.catalina.startup.WebAnnotationSet.loadApplicationAnnotations(WebAnnotationSet.java:56)
        at org.apache.catalina.startup.ContextConfig.applicationAnnotationsConfig(ContextConfig.java:297)
        at org.apache.catalina.startup.ContextConfig.start(ContextConfig.java:1074)
        at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:261)
        at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
        at org.apache.catalina.core.StandardContext.start(StandardContext.java:4377)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:791)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:771)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:526)
        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)
        at org.apache.catalina.core.StandardHost.start(StandardHost.java:722)
        at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
        at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
        at org.apache.catalina.core.StandardService.start(StandardService.java:516)
        at org.apache.catalina.core.StandardServer.start(StandardServer.java:710)
        at org.apache.catalina.startup.Catalina.start(Catalina.java:593)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
       at java.lang.reflect.Method.invoke(Method.java:622)
        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
Aug 13, 2014 1:20:51 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive sweet.war
Aug 13, 2014 1:20:51 PM org.apache.catalina.loader.WebappClassLoader validateJarFile
INFO: validateJarFile(/app001/tomcat6/webapps/sweet/WEB-INF/lib/servlet-api-2.5.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
2014-08-13 13:21:16,830 WARN org.apache.solr.handler.component.SpellCheckComponent - No queryConverter defined, using default converter
Aug 13, 2014 1:21:17 PM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
Aug 13, 2014 1:21:17 PM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8443
Aug 13, 2014 1:21:17 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 27378 ms
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