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

Wed Aug 13 15:51:53 EDT 2014

Hi Neil,
the error in catalina.out is due to a JRE version mismatch (and not a sweet version mismatch).
Make sure your Tomcat is running under Java 1.7 and not 1.6 - sweet.war has a dependency on Java 1.7

Try to fix that first, and see if the other errors disappear.

Cheers
Daniela

Dr. Daniela Bourges-Waldegg
Lead Architect, Harvard Catalyst
Harvard Medical School

Daniela_Bourges at hms.harvard.edu
skype: dbourgesw
phone: 617-432-3126

On Aug 13, 2014, at 15:25, Norman, Neil <neil.norman at vanderbilt.edu> wrote:

> 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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