The web application [ROOT] appears to have started a thread named [JonasBatch] but has failed

[Hyd3k]

Hi I got Jira 7.7.0 and after updating BigPicture Jira was not able to run, I'm getting following error message in catalina.out, any idea how to fix my JIRA installation?

2018-01-17 20:51:41,540 JIRA-Bootstrap ERROR      [c.a.jira.health.HealthChecks] We couldn't start JIRA

2018-01-17 20:51:41,540 JIRA-Bootstrap ERROR      [c.a.jira.health.HealthChecks] An error occurred while trying to start JIRA. We can't give you any more detail right now, we suggest checking the logs for more detail and contacting our support team.

    See our documentation for more information on contacting our support team and creating a support zip.

2018-01-17 20:51:42,346 JIRA-Bootstrap ERROR      [c.a.jira.health.HealthChecks] Could not execute health check, DatabaseConfigurationManager not available.

2018-01-17 20:51:42,346 JIRA-Bootstrap ERROR      [c.a.jira.health.HealthChecks] Could not execute health check, DatabaseConfigurationManager not available.

2018-01-17 20:51:42,347 JIRA-Bootstrap ERROR      [c.a.jira.startup.DefaultJiraLauncher] JIRA has failed to start because of the following errors: [(Event: Level = (EventLevel: fatal) , Key = (EventType: startup-unexpected) , Desc = We couldn't start JIRA , Exception = An error occurred while trying to start JIRA. We can't give you any more detail right now, we suggest checking the logs for more detail and contacting our support team.<br/>See our documentation for more information on contacting our support team and creating a support zip.), (Event: Level = (EventLevel: fatal) , Key = (EventType: database) , Desc = Could not execute health check, DatabaseConfigurationManager not available. , Exception = ]

2018-01-17 20:51:42,351 JIRA-Bootstrap INFO      [c.a.jira.startup.LauncherContextListener] Memory Usage:

2018-01-17 20:51:42,352 localhost-startStop-1 INFO      [c.a.jira.startup.DefaultJiraLauncher] Stopping launchers

2018-01-17 20:51:42,607 localhost-startStop-1 INFO      [c.a.jira.startup.DefaultJiraLauncher] JIRA launchers stopped in 252ms

17-Jan-2018 20:51:42.638 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [JonasBatch] 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.Object.wait(Object.java:502)

 org.objectweb.jonas_timer.TimerManager.batch(TimerManager.java:193)

 org.objectweb.jonas_timer.Batch.run(TimerManager.java:65)

17-Jan-2018 20:51:42.639 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [JonasClock] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:

 java.lang.Thread.sleep(Native Method)

 org.objectweb.jonas_timer.TimerManager.clock(TimerManager.java:142)

 org.objectweb.jonas_timer.Clock.run(TimerManager.java:46)

17-Jan-2018 20:51:42.651 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["https-jsse-nio-8443"]

17-Jan-2018 20:51:42.652 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]

17-Jan-2018 20:51:42.652 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]

17-Jan-2018 20:51:42.653 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["https-jsse-nio-8443"]

[Hyd3k · Accepted solution]

The problem was BigPicture add-on after updating something went wrong and disabled it.

I fixed the issue re enabling it trough the data base.

https://confluence.atlassian.com/jirakb/jira-application-does-not-start-due-to-disabled-bundled-plugin-254738702.html

Thank you for your help!

[Boris Berenberg - Atlas Authority]

The bit about what actually caused the issue is above what you have posted. This isn't enough for us to diagnose the issue.

[Hyd3k]

2018-01-17 21:43:51,719 JIRA-Bootstrap ERROR      [c.a.jira.upgrade.PluginSystemLauncher] A fatal error occured during initialisation. JIRA has been locked.

com.atlassian.jira.InfrastructureException: Error occurred while starting Plugin Manager. Unable to create a tracker when osgi is not running

at com.atlassian.jira.ComponentManager$PluginSystem.earlyStartup(ComponentManager.java:771)

at com.atlassian.jira.ComponentManager.quickStart(ComponentManager.java:199)

at com.atlassian.jira.ComponentManager.start(ComponentManager.java:168)

at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:45)

at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$2(DefaultJiraLauncher.java:143)

at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:304)

at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:199)

at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:135)

at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$0(DefaultJiraLauncher.java:102)

at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)

at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:100)

at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:157)

at java.lang.Thread.run(Thread.java:745)

Caused by: java.lang.IllegalStateException: Unable to create a tracker when osgi is not running

at com.atlassian.plugin.osgi.container.felix.FelixOsgiContainerManager.getServiceTracker(FelixOsgiContainerManager.java:490)

at com.atlassian.plugin.osgi.container.felix.FelixOsgiContainerManager.getServiceTracker(FelixOsgiContainerManager.java:482)

at com.atlassian.plugin.osgi.factory.OsgiBundlePlugin.installInternal(OsgiBundlePlugin.java:262)

at com.atlassian.plugin.impl.AbstractPlugin.install(AbstractPlugin.java:424)

at com.atlassian.plugin.manager.DefaultPluginManager.addPlugins(DefaultPluginManager.java:1181)

at com.atlassian.plugin.manager.DefaultPluginManager.earlyStartup(DefaultPluginManager.java:597)

at com.atlassian.jira.plugin.JiraPluginManager.earlyStartup(JiraPluginManager.java:118)

at com.atlassian.jira.ComponentManager$PluginSystem.earlyStartup(ComponentManager.java:764)

[Hyd3k]

Log file is very big/large, what do you need to troubleshoot?

This just occurred after updating BigPicture from previous not compatible version to current compatible version with Jira 7.7.0.

[Boris Berenberg - Atlas Authority]

There's some error before after the startup and before this which is causing it. I can't tell you what it is or how far back it is.

[Björn Bittins]

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