Error after upgrading to JIRA 7.11.0

[jkwietko]

After upgrade to JIRA 7.11.0 on my server, when I started service, I got the error message "JIRA Software is currently unavailable.

Logs:

2018-07-18 09:12:04,261 localhost-startStop-2 ERROR      [o.e.g.b.e.i.util.concurrent.RunnableTimedExecution] Closing runnable for context NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.upm.application-plugin, config=osgibundle:/META-INF/spring/*.xml) did not finish in 10000ms; consider taking a snapshot and then shutdown the VM in case the thread still hangs
2018-07-18 09:12:04,402 Gemini Blueprint context shutdown thread2 WARN      [o.s.context.annotation.CommonAnnotationBeanPostProcessor] Invocation of destroy method failed on bean with name 'devtoolsWorkflowEventBridge': org.eclipse.gemini.blueprint.service.ServiceUnavailableException: service matching filter=[(&(objectClass=com.atlassian.event.remote.RemoteEventListenerRegistrar)(objectClass=com.atlassian.event.remote.RemoteEventListenerRegistrar))] unavailable
2018-07-18 09:12:14,421 FelixShutdown ERROR      [o.e.g.b.e.i.util.concurrent.RunnableTimedExecution] Closing runnable for context NonValidatingOsgiBundleXmlApplicationContext(bundle=com.onresolve.jira.groovy.groovyrunner, config=osgibundle:/META-INF/spring/*.xml) did not finish in 10000ms; consider taking a snapshot and then shutdown the VM in case the thread still hangs
2018-07-18 09:12:24,253 Gemini Blueprint context shutdown thread1 WARN      [o.s.b.factory.support.DisposableBeanAdapter] Invocation of destroy method failed on bean with name 'marketplaceClientManager': com.atlassian.util.concurrent.LazyReference$InitializationException: org.eclipse.gemini.blueprint.service.ServiceUnavailableException: service matching filter=[(objectClass=com.atlassian.sal.api.ApplicationProperties)] unavailable
2018-07-18 09:12:24,316 Gemini Blueprint context shutdown thread1 INFO      [c.atlassian.agile.support]
    
    *********************************************************************************
    Atlassian GreenHopper v7.11.0-DAILY20180626110825 #79adc01e6e353b6b built 2018-06-26T13:14:31.012+02:00 - plugin stopping...
    *********************************************************************************
    
2018-07-18 09:12:24,425 FelixShutdown ERROR      [o.e.g.b.e.i.util.concurrent.RunnableTimedExecution] Closing runnable for context NonValidatingOsgiBundleXmlApplicationContext(bundle=com.pyxis.greenhopper.jira, config=osgibundle:/META-INF/spring/*.xml) did not finish in 10000ms; consider taking a snapshot and then shutdown the VM in case the thread still hangs
2018-07-18 09:12:34,430 FelixShutdown ERROR      [o.e.g.b.e.i.util.concurrent.RunnableTimedExecution] Closing runnable for context NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.troubleshooting.plugin-jira, config=osgibundle:/META-INF/spring/*.xml) did not finish in 10000ms; consider taking a snapshot and then shutdown the VM in case the thread still hangs
2018-07-18 09:12:34,462 Gemini Blueprint context shutdown thread2 WARN      [o.s.b.factory.support.DisposableBeanAdapter] Invocation of destroy method failed on bean with name 'diagnosticsManager': org.eclipse.gemini.blueprint.service.ServiceUnavailableException: service matching filter=[(objectClass=com.atlassian.activeobjects.external.ActiveObjects)] unavailable
2018-07-18 09:12:44,437 FelixShutdown ERROR      [o.e.g.b.e.i.util.concurrent.RunnableTimedExecution] Closing runnable for context NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.jira.jira-email-processor-plugin, config=osgibundle:/META-INF/spring/*.xml) did not finish in 10000ms; consider taking a snapshot and then shutdown the VM in case the thread still hangs
2018-07-18 09:12:54,320 Gemini Blueprint context shutdown thread1 WARN      [o.s.context.annotation.CommonAnnotationBeanPostProcessor] Invocation of destroy method failed on bean with name 'greenhopper-launcher': org.eclipse.gemini.blueprint.service.ServiceUnavailableException: service matching filter=[(objectClass=com.atlassian.sal.api.scheduling.PluginScheduler)] unavailable
2018-07-18 09:13:04,464 Gemini Blueprint context shutdown thread2 WARN      [o.s.b.factory.support.DisposableBeanAdapter] Invocation of destroy method failed on bean with name 'eventTrackingManager': org.eclipse.gemini.blueprint.service.ServiceUnavailableException: service matching filter=[(objectClass=com.atlassian.sal.api.scheduling.PluginScheduler)] unavailable
2018-07-18 09:13:04,636 Gemini Blueprint context shutdown thread2 WARN      [o.s.b.factory.support.DisposableBeanAdapter] Invocation of destroy method failed on bean with name 'licenseChecker': java.lang.RuntimeException: Retry failed; interrupted while waiting
2018-07-18 09:13:05,917 localhost-startStop-2 ERROR      [o.a.c.c.C.[Catalina].[localhost].[/]] Exception sending context destroyed event to listener instance of class [com.atlassian.jira.startup.LauncherContextListener]
java.lang.NoClassDefFoundError: org/codehaus/groovy/runtime/GroovyCategorySupport$1
    at java.lang.Class.getDeclaringClass0(Native Method)
    at java.lang.Class.getDeclaringClass(Class.java:1235)
    at java.lang.Class.getEnclosingClass(Class.java:1277)
    at java.lang.Class.getCanonicalName(Class.java:1392)
    at com.atlassian.threadlocal.BruteForceThreadLocalCleanup.getPrettyClassName(BruteForceThreadLocalCleanup.java:257)
    at com.atlassian.threadlocal.BruteForceThreadLocalCleanup.checkThreadLocalMapForLeaks(BruteForceThreadLocalCleanup.java:181)
    at com.atlassian.threadlocal.BruteForceThreadLocalCleanup.cleanUpThreadImpl(BruteForceThreadLocalCleanup.java:135)
    at com.atlassian.threadlocal.BruteForceThreadLocalCleanup.cleanupThreadLocals(BruteForceThreadLocalCleanup.java:94)
    at com.atlassian.threadlocal.BruteForceThreadLocalCleanup.cleanUp(BruteForceThreadLocalCleanup.java:63)
    at com.atlassian.jira.startup.DefaultJiraLauncher.cleanupThreadLocals(DefaultJiraLauncher.java:253)
    at com.atlassian.jira.startup.DefaultJiraLauncher.cleanupAfterOurselves(DefaultJiraLauncher.java:218)
    at com.atlassian.jira.startup.DefaultJiraLauncher.stop(DefaultJiraLauncher.java:214)
    at com.atlassian.jira.startup.LauncherContextListener.contextDestroyed(LauncherContextListener.java:211)
    ... 5 filtered
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: Unable to load class 'org.codehaus.groovy.runtime.GroovyCategorySupport$1' because the bundle wiring for com.onresolve.jira.groovy.groovyrunner is no longer valid.
    at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1494)
    at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:75)
    at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1955)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    ... 22 more

[Andy Heinzer]

Hi Jacob,

This log excerpt just shows us that the Jira Software plugin is shutting down.  It doesn't tell us why that is.  It could be that another plugin that provides a dependency failed to load, but there could be other factors as well.

Since you're only seeing this after an upgrade, the common causes tend to be

• Insufficient memory allocated to Jira - commonly happens during upgrades because the new install has default values in the setenv.sh or the windows service.  I'd recommend checking your values again by following the Increasing Jira memory guide.
• Incompatible plugins failed to load.   Also common when upgrading.  I'd recommend the following:

1. Stop Jira
2. move all the files currently in the $JIRAHOME/plugins/installed-plugins/ folder to a temp folder outside the Jira home
3. In the Jira database run the following SQL command to clear any flags that might be preventing plugins from loading

   truncate table pluginstate;

4. start Jira 
5. In Jira, reinstall your plugins by using the UPM in Jira.  For Jira Software/Service Desk this can be done on the Cog Icon- > Applications -> Versions and Licenses page directly.  For all other plugins, this happens on Cog Icon -> Add-ons -> Find new add-ons.   But using this method to reinstall your plugins, we can be more certain that you will be installing compatible versions of everything that work with this newer version of Jira

If you have done both of these steps and you still see the Jira Software is not loading up, I would be interested to see if we can take a closer look at your support zip from Jira (or a complete set of logs) in order to see whats happening.  If you want to post these to a service like google drive or dropbox you can then share the link with us here and I can take a look that way.