how can i get help with jira server error

[Comrax Webmaster]

we working with JIRA software more then 2 years and yaserday i got some "page not found" in all desks.

i try to restart server , check for free space , restart serivces .

Server startup logs are located in /opt/atlassian/jira/logs/catalina.out
Using CATALINA_BASE: /opt/atlassian/jira
Using CATALINA_HOME: /opt/atlassian/jira
Using CATALINA_TMPDIR: /opt/atlassian/jira/temp
Using JRE_HOME: /opt/atlassian/jira/jre/
Using CLASSPATH: /opt/atlassian/jira/bin/bootstrap.jar:/opt/atlassian/jira/bin/tomcat-juli.jar
Using CATALINA_PID: /opt/atlassian/jira/work/catalina.pid
Existing PID file found during start.
Removing/clearing stale PID file.
Tomcat started.

i dont know what to do more ... 

etgar@comrax.com

[Jonas Andersson]

Don't have anything solid to offer you, so i would first suggest you start a case with atlassian. Since the server is down, set level 1/level2 during case creation. If this is a VM i suggest you clone it asap, in order to preserve a copy as close to the working state as you can before fiddling any more with it.

While waiting for response, check these few things, maybe you get lucky and stumble over an answer.

• When was it upgraded to 7.1.7, can these issues have started then?
• Do you run puppet/ansible/cfengine/chef or something that might have change JDK/JRE? if the JRE that starts JIRA is /usr/bin/java, verify that it's running on a supported java.
• did the server run out of diskspace at some point during a plugin upgrade?
  
  

[Comrax Webmaster]

:58)
at com.atlassian.plugin.osgi.factory.OsgiPluginFactory.getChainedModuleDescriptorFactory(OsgiPluginFactory.java:321)
at com.atlassian.plugin.osgi.factory.OsgiPluginFactory.create(OsgiPluginFactory.java:222)
at com.atlassian.jira.plugin.MasterPluginFactory.create(MasterPluginFactory.java:73)
at com.atlassian.plugin.loaders.ScanningPluginLoader.deployPluginFromUnit(ScanningPluginLoader.java:142)
at com.atlassian.plugin.loaders.ScanningPluginLoader.loadAllPlugins(ScanningPluginLoader.java:87)
at com.atlassian.plugin.loaders.PermissionCheckingPluginLoader.loadAllPlugins(PermissionCheckingPluginLoader.java:28)
at com.atlassian.plugin.manager.DefaultPluginManager.earlyStartup(DefaultPluginManager.java:524)
at com.atlassian.jira.plugin.JiraPluginManager.earlyStartup(JiraPluginManager.java:118)
at com.atlassian.jira.ComponentManager$PluginSystem.earlyStartup(ComponentManager.java:610)
at com.atlassian.jira.ComponentManager.quickStart(ComponentManager.java:188)
at com.atlassian.jira.ComponentManager.start(ComponentManager.java:157)
at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:43)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$831(DefaultJiraLauncher.java:146)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:298)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:194)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:137)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$829(DefaultJiraLauncher.java:103)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:101)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:115)
at java.lang.Thread.run(Thread.java:745)
2016-11-29 15:13:38,747 JIRA-Bootstrap ERROR [c.a.plugin.loaders.ScanningPluginLoader] Unable to deploy plugin 'com.atlassian.jira.plugins.jira-importers-plugin' from 'Unit: /var/atlassian/application-data/jira/plugins/installed-plugins/plugin.6750927075233308454.jira-importers-plugin-6.2.7.jar (1416323600000)'.
2016-11-29 15:13:38,747 JIRA-Bootstrap ERROR [c.a.plugin.loaders.ScanningPluginLoader] Because of the following exception:
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.OsgiPluginFactory$1.create(OsgiPluginFactory.java:116)
at com.atlassian.plugin.osgi.factory.OsgiChainedModuleDescriptorFactoryCreator.create(OsgiChainedModuleDescriptorFactoryCreator.java:58)
at com.atlassian.plugin.osgi.factory.OsgiPluginFactory.getChainedModuleDescriptorFactory(OsgiPluginFactory.java:321)
at com.atlassian.plugin.osgi.factory.OsgiPluginFactory.create(OsgiPluginFactory.java:222)
at com.atlassian.jira.plugin.MasterPluginFactory.create(MasterPluginFactory.java:73)
at com.atlassian.plugin.loaders.ScanningPluginLoader.deployPluginFromUnit(ScanningPluginLoader.java:142)
at com.atlassian.plugin.loaders.ScanningPluginLoader.loadAllPlugins(ScanningPluginLoader.java:87)
at com.atlassian.plugin.loaders.PermissionCheckingPluginLoader.loadAllPlugins(PermissionCheckingPluginLoader.java:28)
at com.atlassian.plugin.manager.DefaultPluginManager.earlyStartup(DefaultPluginManager.java:524)
at com.atlassian.jira.plugin.JiraPluginManager.earlyStartup(JiraPluginManager.java:118)
at com.atlassian.jira.ComponentManager$PluginSystem.earlyStartup(ComponentManager.java:610)
at com.atlassian.jira.ComponentManager.quickStart(ComponentManager.java:188)
at com.atlassian.jira.ComponentManager.start(ComponentManager.java:157)
at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:43)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$831(DefaultJiraLauncher.java:146)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:298)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:194)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:137)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$829(DefaultJiraLauncher.java:103)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:101)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:115)
at java.lang.Thread.run(Thread.java:745)
2016-11-29 15:13:38,755 JIRA-Bootstrap ERROR [c.a.plugin.loaders.ScanningPluginLoader] Unable to deploy plugin 'com.atlassian.jira.plugins.jira-importers-bitbucket-plugin' from 'Unit: /var/atlassian/application-data/jira/plugins/installed-plugins/plugin.7638654719043265672.jira-importers-bitbucket-plugin-1.0.10.jar (1416322625000)'.
2016-11-29 15:13:38,755 JIRA-Bootstrap ERROR [c.a.plugin.loaders.ScanningPluginLoader] Because of the following exception:
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.OsgiPluginFactory$1.create(OsgiPluginFactory.java:116)
at com.atlassian.plugin.osgi.factory.OsgiChainedModuleDescriptorFactoryCreator.create(OsgiChainedModuleDescriptorFactoryCreator.java:58)
at com.atlassian.plugin.osgi.factory.OsgiPluginFactory.getChainedModuleDescriptorFactory(OsgiPluginFactory.java:321)
at com.atlassian.plugin.osgi.factory.OsgiPluginFactory.create(OsgiPluginFactory.java:222)
at com.atlassian.jira.plugin.MasterPluginFactory.create(MasterPluginFactory.java:73)
at com.atlassian.plugin.loaders.ScanningPluginLoader.deployPluginFromUnit(ScanningPluginLoader.java:142)
at com.atlassian.plugin.loaders.ScanningPluginLoader.loadAllPlugins(ScanningPluginLoader.java:87)
at com.atlassian.plugin.loaders.PermissionCheckingPluginLoader.loadAllPlugins(PermissionCheckingPluginLoader.java:28)
at com.atlassian.plugin.manager.DefaultPluginManager.earlyStartup(DefaultPluginManager.java:524)
at com.atlassian.jira.plugin.JiraPluginManager.earlyStartup(JiraPluginManager.java:118)
at com.atlassian.jira.ComponentManager$PluginSystem.earlyStartup(ComponentManager.java:610)
at com.atlassian.jira.ComponentManager.quickStart(ComponentManager.java:188)
at com.atlassian.jira.ComponentManager.start(ComponentManager.java:157)
at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:43)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$831(DefaultJiraLauncher.java:146)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:298)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:194)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:137)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$829(DefaultJiraLauncher.java:103)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:101)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:115)
at java.lang.Thread.run(Thread.java:745)
2016-11-29 15:13:38,792 JIRA-Bootstrap ERROR [c.a.plugin.loaders.ScanningPluginLoader] Unable to deploy plugin 'com.atlassian.upm.atlassian-universal-plugin-manager-plugin' from 'Unit: /var/atlassian/application-data/jira/plugins/installed-plugins/plugin.8125811775098492201.atlassian-universal-plugin-manager-plugin-2.18.2.jar (1416322462000)'.
2016-11-29 15:13:38,793 JIRA-Bootstrap ERROR [c.a.plugin.loaders.ScanningPluginLoader] Because of the following exception:
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.OsgiPluginFactory$1.create(OsgiPluginFactory.java:116)
at com.atlassian.plugin.osgi.factory.OsgiChainedModuleDescriptorFactoryCreator.create(OsgiChainedModuleDescriptorFactoryCreator.java:58)
at com.atlassian.plugin.osgi.factory.OsgiPluginFactory.getChainedModuleDescriptorFactory(OsgiPluginFactory.java:321)
at com.atlassian.plugin.osgi.factory.OsgiPluginFactory.create(OsgiPluginFactory.java:222)
at com.atlassian.jira.plugin.MasterPluginFactory.create(MasterPluginFactory.java:73)
at com.atlassian.plugin.loaders.ScanningPluginLoader.deployPluginFromUnit(ScanningPluginLoader.java:142)
at com.atlassian.plugin.loaders.ScanningPluginLoader.loadAllPlugins(ScanningPluginLoader.java:87)
at com.atlassian.plugin.loaders.PermissionCheckingPluginLoader.loadAllPlugins(PermissionCheckingPluginLoader.java:28)
at com.atlassian.plugin.manager.DefaultPluginManager.earlyStartup(DefaultPluginManager.java:524)
at com.atlassian.jira.plugin.JiraPluginManager.earlyStartup(JiraPluginManager.java:118)
at com.atlassian.jira.ComponentManager$PluginSystem.earlyStartup(ComponentManager.java:610)
at com.atlassian.jira.ComponentManager.quickStart(ComponentManager.java:188)
at com.atlassian.jira.ComponentManager.start(ComponentManager.java:157)
at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:43)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$831(DefaultJiraLauncher.java:146)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:298)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:194)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:137)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$829(DefaultJiraLauncher.java:103)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:101)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:115)
at java.lang.Thread.run(Thread.java:745)
2016-11-29 15:13:38,805 JIRA-Bootstrap ERROR [c.a.plugin.loaders.ScanningPluginLoader] Unable to deploy plugin 'com.atlassian.support.stp' from 'Unit: /var/atlassian/application-data/jira/plugins/installed-plugins/stp-3.5.20.jar (1416323112000)'.
2016-11-29 15:13:38,805 JIRA-Bootstrap ERROR [c.a.plugin.loaders.ScanningPluginLoader] Because of the following exception:
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.OsgiPluginFactory$1.create(OsgiPluginFactory.java:116)
at com.atlassian.plugin.osgi.factory.OsgiChainedModuleDescriptorFactoryCreator.create(OsgiChainedModuleDescriptorFactoryCreator.java:58)
at com.atlassian.plugin.osgi.factory.OsgiPluginFactory.getChainedModuleDescriptorFactory(OsgiPluginFactory.java:321)
at com.atlassian.plugin.osgi.factory.OsgiPluginFactory.create(OsgiPluginFactory.java:222)
at com.atlassian.jira.plugin.MasterPluginFactory.create(MasterPluginFactory.java:73)
at com.atlassian.plugin.loaders.ScanningPluginLoader.deployPluginFromUnit(ScanningPluginLoader.java:142)
at com.atlassian.plugin.loaders.ScanningPluginLoader.loadAllPlugins(ScanningPluginLoader.java:87)
at com.atlassian.plugin.loaders.PermissionCheckingPluginLoader.loadAllPlugins(PermissionCheckingPluginLoader.java:28)
at com.atlassian.plugin.manager.DefaultPluginManager.earlyStartup(DefaultPluginManager.java:524)
at com.atlassian.jira.plugin.JiraPluginManager.earlyStartup(JiraPluginManager.java:118)
at com.atlassian.jira.ComponentManager$PluginSystem.earlyStartup(ComponentManager.java:610)
at com.atlassian.jira.ComponentManager.quickStart(ComponentManager.java:188)
at com.atlassian.jira.ComponentManager.start(ComponentManager.java:157)
at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:43)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$831(DefaultJiraLauncher.java:146)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:298)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:194)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:137)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$829(DefaultJiraLauncher.java:103)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:101)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:115)
at java.lang.Thread.run(Thread.java:745)
2016-11-29 15:13:38,857 JIRA-Bootstrap ERROR [c.a.jira.upgrade.PluginSystemLauncher] A fatal error occured during initialisation. JIRA has been locked.
com.atlassian.jira.InfrastructureException: Error occurred while starting Plugin Manager. Unable to create a tracker when osgi is not running
at com.atlassian.jira.ComponentManager$PluginSystem.earlyStartup(ComponentManager.java:617)
at com.atlassian.jira.ComponentManager.quickStart(ComponentManager.java:188)
at com.atlassian.jira.ComponentManager.start(ComponentManager.java:157)
at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:43)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$831(DefaultJiraLauncher.java:146)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:298)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:194)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:137)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$829(DefaultJiraLauncher.java:103)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:101)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:115)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalStateException: Unable to create a tracker when osgi is not running
at com.atlassian.plugin.osgi.container.felix.FelixOsgiContainerManager.getServiceTracker(FelixOsgiContainerManager.java:490)
at com.atlassian.plugin.osgi.container.felix.FelixOsgiContainerManager.getServiceTracker(FelixOsgiContainerManager.java:482)
at com.atlassian.plugin.osgi.factory.OsgiBundlePlugin.installInternal(OsgiBundlePlugin.java:262)
at com.atlassian.plugin.impl.AbstractPlugin.install(AbstractPlugin.java:423)
at com.atlassian.plugin.manager.DefaultPluginManager.addPlugins(DefaultPluginManager.java:1154)
at com.atlassian.plugin.manager.DefaultPluginManager.earlyStartup(DefaultPluginManager.java:573)
at com.atlassian.jira.plugin.JiraPluginManager.earlyStartup(JiraPluginManager.java:118)
at com.atlassian.jira.ComponentManager$PluginSystem.earlyStartup(ComponentManager.java:610)
... 12 more
2016-11-29 15:13:38,901 JIRA-Bootstrap INFO [c.a.jira.tenancy.DefaultTenantManager] Instance has a tenant. Now running [Tenanted launchers]
2016-11-29 15:13:38,904 JIRA-Bootstrap INFO [c.a.jira.startup.DefaultInstantUpgradeManager] Now running [Late startup launchers]
2016-11-29 15:13:38,904 JIRA-Bootstrap INFO [c.a.jira.upgrade.ConsistencyCheckImpl] Checking JIRA consistency
2016-11-29 15:13:38,944 JIRA-Bootstrap ERROR [c.a.jira.upgrade.ConsistencyCheckImpl] An error occurred during the consistency check
java.lang.IllegalStateException: It is illegal to call the ServiceManager before all components are loaded. Please use interface com.atlassian.jira.extension.Startable to get notified when JIRA has started.
at com.atlassian.jira.service.DefaultServiceManager.getServiceCache(DefaultServiceManager.java:519)
at com.atlassian.jira.service.DefaultServiceManager.getServices(DefaultServiceManager.java:116)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.getServices(ConsistencyCheckImpl.java:152)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.ensureSingleService(ConsistencyCheckImpl.java:439)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.checkMailListenerAndService(ConsistencyCheckImpl.java:325)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.checkDataConsistency(ConsistencyCheckImpl.java:197)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.checkConsistency(ConsistencyCheckImpl.java:189)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.initialise(ConsistencyCheckImpl.java:158)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postTenantArrived$833(DefaultJiraLauncher.java:176)
at com.atlassian.jira.startup.DefaultInstantUpgradeManager$StatupTask.run(DefaultInstantUpgradeManager.java:113)
at com.atlassian.jira.startup.DefaultInstantUpgradeManager.runTask(DefaultInstantUpgradeManager.java:46)
at com.atlassian.jira.startup.DefaultInstantUpgradeManager.doNowOrWhenInstanceBecomesActive(DefaultInstantUpgradeManager.java:35)
at com.atlassian.jira.startup.DefaultJiraLauncher.postTenantArrived(DefaultJiraLauncher.java:173)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDBActivated$832(DefaultJiraLauncher.java:161)
at com.atlassian.jira.tenancy.DefaultTenantManager.doNowOrWhenTenantArrives(DefaultTenantManager.java:55)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDBActivated(DefaultJiraLauncher.java:158)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$831(DefaultJiraLauncher.java:147)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:298)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:194)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:137)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$829(DefaultJiraLauncher.java:103)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:101)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:115)
at java.lang.Thread.run(Thread.java:745)
2016-11-29 15:13:39,743 JIRA-Bootstrap ERROR [c.a.jira.startup.JiraStartupLogger] Cannnot obtain JIRA system information
java.lang.IllegalStateException: It is illegal to call the ServiceManager before all components are loaded. Please use interface com.atlassian.jira.extension.Startable to get notified when JIRA has started.
at com.atlassian.jira.service.DefaultServiceManager.getServiceCache(DefaultServiceManager.java:519)
at com.atlassian.jira.service.DefaultServiceManager.getServices(DefaultServiceManager.java:116)
at com.atlassian.jira.startup.JiraSystemInfo.obtainServices(JiraSystemInfo.java:536)
at com.atlassian.jira.startup.JiraStartupLogger.printStartedMessage(JiraStartupLogger.java:132)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.printJIRAStartupMessage(ConsistencyCheckImpl.java:172)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.initialise(ConsistencyCheckImpl.java:162)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postTenantArrived$833(DefaultJiraLauncher.java:176)
at com.atlassian.jira.startup.DefaultInstantUpgradeManager$StatupTask.run(DefaultInstantUpgradeManager.java:113)
at com.atlassian.jira.startup.DefaultInstantUpgradeManager.runTask(DefaultInstantUpgradeManager.java:46)
at com.atlassian.jira.startup.DefaultInstantUpgradeManager.doNowOrWhenInstanceBecomesActive(DefaultInstantUpgradeManager.java:35)
at com.atlassian.jira.startup.DefaultJiraLauncher.postTenantArrived(DefaultJiraLauncher.java:173)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDBActivated$832(DefaultJiraLauncher.java:161)
at com.atlassian.jira.tenancy.DefaultTenantManager.doNowOrWhenTenantArrives(DefaultTenantManager.java:55)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDBActivated(DefaultJiraLauncher.java:158)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$831(DefaultJiraLauncher.java:147)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:298)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:194)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:137)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$829(DefaultJiraLauncher.java:103)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:101)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:115)
at java.lang.Thread.run(Thread.java:745)
2016-11-29 15:13:39,747 JIRA-Bootstrap WARN [c.a.jira.startup.JiraStartupLogger]

********************************************************************************************************************************************************************************************************
The following plugins failed to load:
com.atlassian.applinks.applinks-plugin: Unable to create a tracker when osgi is not running
com.atlassian.applinks.applinks-cors-plugin: Unable to create a tracker when osgi is not running
com.atlassian.analytics.analytics-whitelist: Unable to create a tracker when osgi is not running
com.atlassian.administration.atlassian-admin-quicksearch-jira: Unable to create a tracker when osgi is not running
com.atlassian.applinks.applinks-basicauth-plugin: Unable to create a tracker when osgi is not running
com.atlassian.activeobjects.activeobjects-plugin: Unable to create a tracker when osgi is not running
com.atlassian.atlassian-failure-cache-plugin: Unable to create a tracker when osgi is not running
com.atlassian.applinks.applinks-trustedapps-plugin: Unable to create a tracker when osgi is not running
com.atlassian.auiplugin: Unable to create a tracker when osgi is not running
com.atlassian.analytics.analytics-client: Unable to create a tracker when osgi is not running
com.atlassian.applinks.applinks-oauth-plugin: Unable to create a tracker when osgi is not running
********************************************************************************************************************************************************************************************************

2016-11-29 15:13:39,748 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]

**********************************************************************************
JIRA 7.1.7 build: 71011 started. You can now access JIRA through your web browser.
**********************************************************************************

2016-11-29 15:13:39,783 JIRA-Bootstrap ERROR [c.a.jira.upgrade.UpgradeLauncher] Skipping, JIRA is locked.
2016-11-29 15:13:39,784 JIRA-Bootstrap INFO [c.a.jira.scheduler.JiraSchedulerLauncher] JIRA Scheduler not started: JIRA startup checklist failed.
2016-11-29 15:13:40,397 JIRA-Bootstrap ERROR [c.a.j.s.services.analytics.JiraStartStopAnalyticHelper] Error trying to grab analytics from [com.atlassian.jira.service.services.analytics.start.WorkflowAnalyticTask]
java.lang.NullPointerException
at com.atlassian.jira.workflow.DefaultWorkflowSchemeManager.getActiveWorkflowNames(DefaultWorkflowSchemeManager.java:394)
at com.atlassian.jira.workflow.OSWorkflowManager.getSchemeActiveWorkflows(OSWorkflowManager.java:175)
at com.atlassian.jira.workflow.OSWorkflowManager.getActiveWorkflows(OSWorkflowManager.java:161)
at com.atlassian.jira.service.services.analytics.start.WorkflowAnalyticTask.getAnalytics(WorkflowAnalyticTask.java:34)
at com.atlassian.jira.service.services.analytics.JiraStartStopAnalyticHelper.getOnStartUsageStats(JiraStartStopAnalyticHelper.java:41)
at com.atlassian.jira.startup.AnalyticsLauncher.start(AnalyticsLauncher.java:26)
at com.atlassian.jira.startup.ActiveServicesLauncher.start(ActiveServicesLauncher.java:56)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postTenantArrived$833(DefaultJiraLauncher.java:180)
at com.atlassian.jira.startup.DefaultInstantUpgradeManager$StatupTask.run(DefaultInstantUpgradeManager.java:113)
at com.atlassian.jira.startup.DefaultInstantUpgradeManager.runTask(DefaultInstantUpgradeManager.java:46)
at com.atlassian.jira.startup.DefaultInstantUpgradeManager.doNowOrWhenInstanceBecomesActive(DefaultInstantUpgradeManager.java:35)
at com.atlassian.jira.startup.DefaultJiraLauncher.postTenantArrived(DefaultJiraLauncher.java:173)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDBActivated$832(DefaultJiraLauncher.java:161)
at com.atlassian.jira.tenancy.DefaultTenantManager.doNowOrWhenTenantArrives(DefaultTenantManager.java:55)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDBActivated(DefaultJiraLauncher.java:158)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$831(DefaultJiraLauncher.java:147)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:298)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:194)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:137)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$829(DefaultJiraLauncher.java:103)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:101)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:115)
at java.lang.Thread.run(Thread.java:745)
2016-11-29 15:13:40,978 JIRA-Bootstrap INFO [c.a.j.index.ha.DefaultIndexRecoveryManager] Latest index date: {2016-11-28 09:20:47}, Latest DB date: {2016-11-28 09:20:47}
2016-11-29 15:13:41,084 JIRA-Bootstrap INFO [c.a.jira.startup.DefaultInstantUpgradeManager] Late startup launchers took 2s
2016-11-29 15:13:41,104 JIRA-Bootstrap ERROR [c.a.jira.startup.LauncherContextListener] Unable to start JIRA.
java.lang.IllegalStateException: Abnormal system startup detected
at com.atlassian.jira.startup.LauncherContextListener.initDone(LauncherContextListener.java:146)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:128)
at java.lang.Thread.run(Thread.java:745)
2016-11-29 15:13:41,111 JIRA Warmer Thread:thread-1 INFO [c.a.jira.i18n.I18nWarmer] Init i18n cache
2016-11-29 15:13:41,123 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 96 MiB. Committed: 477 MiB. Max: 733 MiB
Non-heap memory : Used: 101 MiB. Committed: 104 MiB. Max: 1264 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 197 MiB. Committed: 581 MiB. Max: 1997 MiB
---------------------------------------------------------------------------------
2016-11-29 15:13:41,123 localhost-startStop-1 INFO [c.a.jira.startup.DefaultJiraLauncher] Stopping launchers
2016-11-29 15:13:41,163 localhost-startStop-1 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.IllegalStateException: It is illegal to call the ServiceManager before all components are loaded. Please use interface com.atlassian.jira.extension.Startable to get notified when JIRA has started.
at com.atlassian.jira.service.DefaultServiceManager.getServiceCache(DefaultServiceManager.java:519)
at com.atlassian.jira.service.DefaultServiceManager.getServices(DefaultServiceManager.java:116)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.getServices(ConsistencyCheckImpl.java:152)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.destroy(ConsistencyCheckImpl.java:73)
at com.atlassian.jira.startup.DefaultJiraLauncher.stop(DefaultJiraLauncher.java:208)
at com.atlassian.jira.startup.LauncherContextListener.contextDestroyed(LauncherContextListener.java:161)
... 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)
Exception in thread "Modification Check:thread-1" java.lang.NullPointerException
at com.atlassian.jira.cache.HashRegistryCacheImpl$1.getResourceByPath(HashRegistryCacheImpl.java:37)
at com.atlassian.modzdetector.DefaultStreamMapper.mapStream(DefaultStreamMapper.java:33)
at com.atlassian.modzdetector.ModzDetector.checkResource(ModzDetector.java:321)
at com.atlassian.modzdetector.ModzDetector.checkRegistry(ModzDetector.java:207)
at com.atlassian.modzdetector.ModzDetector.getModifiedFiles(ModzDetector.java:88)
at com.atlassian.modzdetector.ModzDetector.getModifiedFiles(ModzDetector.java:64)
at com.atlassian.jira.cache.HashRegistryCacheImpl.getModifications(HashRegistryCacheImpl.java:52)
at com.atlassian.jira.startup.JiraStartupLogger$ModificationCheck.run(JiraStartupLogger.java:195)
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)
2016-11-29 15:13:41,257 JIRA Warmer Thread:thread-1 INFO [c.a.jira.i18n.I18nWarmer] Initialised i18n cache in 146
29-Nov-2016 15:13:41.265 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [Abandoned connection cleanup thread] 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.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
com.mysql.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:41)
29-Nov-2016 15:13:41.267 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [commons-pool-EvictionTimer] 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.util.TimerThread.mainLoop(Timer.java:552)
java.util.TimerThread.run(Timer.java:505)
29-Nov-2016 15:13:41.269 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] 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. Stack trace of thread:
java.lang.Object.wait(Native Method)
java.util.TimerThread.mainLoop(Timer.java:552)
java.util.TimerThread.run(Timer.java:505)
29-Nov-2016 15:13:41.270 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)
29-Nov-2016 15:13:41.271 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)
29-Nov-2016 15:13:41.273 SEVERE [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.checkThreadLocalMapForLeaks The web application [ROOT] created a ThreadLocal with key of type [com.atlassian.jira.security.JiraAuthenticationContextImpl$1] (value [com.atlassian.jira.security.JiraAuthenticationContextImpl$1@250d9e95]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
29-Nov-2016 15:13:41.273 SEVERE [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.checkThreadLocalMapForLeaks The web application [ROOT] created a ThreadLocal with key of type [com.atlassian.instrumentation.operations.ThreadLocalOpTimerFactory$1] (value [com.atlassian.instrumentation.operations.ThreadLocalOpTimerFactory$1@3c63c8c]) and a value of type [com.atlassian.instrumentation.operations.registry.OpRegistry] (value [com.atlassian.instrumentation.operations.registry.OpRegistry@22a9295f {db.reads=OpCounter{name='db.reads', invocationCount=2, elapsedTotal=3955057, elapsedMin=413580, elapsedMax=3541477, resultSetSize=0, cpuTotal=0, cpuMin=0, cpuMax=0}, db.conns=OpCounter{name='db.conns', invocationCount=2, elapsedTotal=10699961, elapsedMin=4815997, elapsedMax=5883964, resultSetSize=0, cpuTotal=0, cpuMin=0, cpuMax=0}}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
29-Nov-2016 15:13:41.294 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
29-Nov-2016 15:13:41.299 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
29-Nov-2016 15:14:08.527 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.0.32
29-Nov-2016 15:14:08.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Feb 2 2016 19:34:53 UTC
29-Nov-2016 15:14:08.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.0.32.0
29-Nov-2016 15:14:08.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
29-Nov-2016 15:14:08.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 3.13.0-95-generic
29-Nov-2016 15:14:08.530 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
29-Nov-2016 15:14:08.531 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /opt/atlassian/jira/jre
29-Nov-2016 15:14:08.531 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_74-b02
29-Nov-2016 15:14:08.531 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
29-Nov-2016 15:14:08.531 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /opt/atlassian/jira
29-Nov-2016 15:14:08.531 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /opt/atlassian/jira
29-Nov-2016 15:14:08.532 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties
29-Nov-2016 15:14:08.532 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
29-Nov-2016 15:14:08.532 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms384m
29-Nov-2016 15:14:08.533 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx768m
29-Nov-2016 15:14:08.533 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
29-Nov-2016 15:14:08.533 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.standalone=JIRA
29-Nov-2016 15:14:08.533 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true
29-Nov-2016 15:14:08.533 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dmail.mime.decodeparameters=true
29-Nov-2016 15:14:08.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
29-Nov-2016 15:14:08.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDateStamps
29-Nov-2016 15:14:08.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow
29-Nov-2016 15:14:08.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.endorsed.dirs=/opt/atlassian/jira/endorsed
29-Nov-2016 15:14:08.534 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/opt/atlassian/jira
29-Nov-2016 15:14:08.535 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/opt/atlassian/jira
29-Nov-2016 15:14:08.535 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/opt/atlassian/jira/temp
29-Nov-2016 15:14:08.535 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
29-Nov-2016 15:14:08.881 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
29-Nov-2016 15:14:08.919 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
29-Nov-2016 15:14:08.924 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 1205 ms
29-Nov-2016 15:14:08.942 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service Catalina
29-Nov-2016 15:14:08.942 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.0.32

2016-11-29 15:14:38,740 localhost-startStop-1 INFO [c.a.jira.startup.DefaultJiraLauncher] Stopping launchers
2016-11-29 15:14:38,773 localhost-startStop-1 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.IllegalStateException: It is illegal to call the ServiceManager before all components are loaded. Please use interface com.atlassian.jira.extension.Startable to get notified when JIRA has started.
at com.atlassian.jira.service.DefaultServiceManager.getServiceCache(DefaultServiceManager.java:519)
at com.atlassian.jira.service.DefaultServiceManager.getServices(DefaultServiceManager.java:116)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.getServices(ConsistencyCheckImpl.java:152)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.destroy(ConsistencyCheckImpl.java:73)
at com.atlassian.jira.startup.DefaultJiraLauncher.stop(DefaultJiraLauncher.java:208)
at com.atlassian.jira.startup.LauncherContextListener.contextDestroyed(LauncherContextListener.java:161)
... 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)
Exception in thread "Modification Check:thread-1" java.lang.NullPointerException
at com.atlassian.jira.cache.HashRegistryCacheImpl$1.getResourceByPath(HashRegistryCacheImpl.java:37)
at com.atlassian.jira.cache.HashRegistryCacheImpl$1.getResourceFromClasspath(HashRegistryCacheImpl.java:29)
at com.atlassian.modzdetector.DefaultStreamMapper.mapStream(DefaultStreamMapper.java:28)
at com.atlassian.modzdetector.ModzDetector.checkResource(ModzDetector.java:321)
at com.atlassian.modzdetector.ModzDetector.checkRegistry(ModzDetector.java:207)
at com.atlassian.modzdetector.ModzDetector.getModifiedFiles(ModzDetector.java:88)
at com.atlassian.modzdetector.ModzDetector.getModifiedFiles(ModzDetector.java:64)
at com.atlassian.jira.cache.HashRegistryCacheImpl.getModifications(HashRegistryCacheImpl.java:52)
at com.atlassian.jira.startup.JiraStartupLogger$ModificationCheck.run(JiraStartupLogger.java:195)
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)
2016-11-29 15:14:38,874 JIRA Warmer Thread:thread-1 INFO [c.a.jira.i18n.I18nWarmer] Initialised i18n cache in 155
29-Nov-2016 15:14:38.881 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [Abandoned connection cleanup thread] 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.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
com.mysql.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:41)
29-Nov-2016 15:14:38.883 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [commons-pool-EvictionTimer] 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.util.TimerThread.mainLoop(Timer.java:552)
java.util.TimerThread.run(Timer.java:505)
29-Nov-2016 15:14:38.885 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] 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. Stack trace of thread:
java.lang.Object.wait(Native Method)
java.util.TimerThread.mainLoop(Timer.java:552)
java.util.TimerThread.run(Timer.java:505)
29-Nov-2016 15:14:38.886 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)
29-Nov-2016 15:14:38.887 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)
29-Nov-2016 15:14:38.890 SEVERE [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.checkThreadLocalMapForLeaks The web application [ROOT] created a ThreadLocal with key of type [com.atlassian.jira.security.JiraAuthenticationContextImpl$1] (value [com.atlassian.jira.security.JiraAuthenticationContextImpl$1@40d17b33]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
29-Nov-2016 15:14:38.890 SEVERE [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.checkThreadLocalMapForLeaks The web application [ROOT] created a ThreadLocal with key of type [com.atlassian.instrumentation.operations.ThreadLocalOpTimerFactory$1] (value [com.atlassian.instrumentation.operations.ThreadLocalOpTimerFactory$1@1c1282ef]) and a value of type [com.atlassian.instrumentation.operations.registry.OpRegistry] (value [com.atlassian.instrumentation.operations.registry.OpRegistry@f31f6a3 {db.reads=OpCounter{name='db.reads', invocationCount=2, elapsedTotal=590047, elapsedMin=195060, elapsedMax=394987, resultSetSize=0, cpuTotal=0, cpuMin=0, cpuMax=0}, db.conns=OpCounter{name='db.conns', invocationCount=2, elapsedTotal=2823987, elapsedMin=495552, elapsedMax=2328435, resultSetSize=0, cpuTotal=0, cpuMin=0, cpuMax=0}}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
29-Nov-2016 15:14:38.923 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
29-Nov-2016 15:14:38.952 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]

[Kacper Kustra]

What do you have in atlassian-jira.log ?