Jira will not start

Question

Hello, I'm having an issue with Jira starting - when trying to access our site I get a connection refused return message. To me, this sounds like the application just simple isn't running. Any responses are greatly appreciated. Here's the catalina.out: 2022-08-10 14:00:05,491 JIRA-Bootstrap ERROR [c.a.jira.upgrade.PluginSystemLauncher] A fatal error occured during initialisation. JIRA has been locked. com.atlassian.plugin.osgi.container.OsgiContainerException: Unable to clean the cache directory: /var/atlassian/application-data/jira/plugins/.osgi-plugins/felix at com.atlassian.plugin.osgi.container.impl.DefaultOsgiPersistentCache.validate(DefaultOsgiPersistentCache.java:71) at com.atlassian.plugin.osgi.container.impl.DefaultOsgiPersistentCache.(DefaultOsgiPersistentCache.java:38) at com.atlassian.jira.plugin.PluginPath$JiraHomeAdapter.(PluginPath.java:135) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ... 1 filtered at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.picocontainer.injectors.AbstractInjector.newInstance(AbstractInjector.java:145) at org.picocontainer.injectors.ConstructorInjector$1.run(ConstructorInjector.java:342) at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:270) at org.picocontainer.injectors.ConstructorInjector.getComponentInstance(ConstructorInjector.java:364) at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64) at org.picocontainer.behaviors.Stored.getComponentInstance(Stored.java:91) at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64) at org.picocontainer.behaviors.Locked.getComponentInstance(Locked.java:40) at org.picocontainer.DefaultPicoContainer.getInstance(DefaultPicoContainer.java:698) at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:646) at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:631) at org.picocontainer.parameters.BasicComponentParameter$1.resolveInstance(BasicComponentParameter.java:118) at org.picocontainer.parameters.ComponentParameter$1.resolveInstance(ComponentParameter.java:136) at org.picocontainer.injectors.SingleMemberInjector.getParameter(SingleMemberInjector.java:78) at org.picocontainer.injectors.ConstructorInjector$CtorAndAdapters.getParameterArguments(ConstructorInjector.java:309) at org.picocontainer.injectors.ConstructorInjector$1.run(ConstructorInjector.java:335) at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:270) at org.picocontainer.injectors.ConstructorInjector.getComponentInstance(ConstructorInjector.java:364) at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64) at org.picocontainer.behaviors.Stored.getComponentInstance(Stored.java:91) at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64) at org.picocontainer.behaviors.Locked.getComponentInstance(Locked.java:40) at org.picocontainer.DefaultPicoContainer.getInstance(DefaultPicoContainer.java:698) at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:646) at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:631) at org.picocontainer.parameters.BasicComponentParameter$1.resolveInstance(BasicComponentParameter.java:118) at org.picocontainer.parameters.ComponentParameter$1.resolveInstance(ComponentParameter.java:136) at org.picocontainer.injectors.SingleMemberInjector.getParameter(SingleMemberInjector.java:78) at org.picocontainer.injectors.ConstructorInjector$CtorAndAdapters.getParameterArguments(ConstructorInjector.java:309) at org.picocontainer.injectors.ConstructorInjector$1.run(ConstructorInjector.java:335) at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:270) at org.picocontainer.injectors.ConstructorInjector.getComponentInstance(ConstructorInjector.java:364) at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64) at org.picocontainer.behaviors.Stored.getComponentInstance(Stored.java:91) at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64) at org.picocontainer.behaviors.Locked.getComponentInstance(Locked.java:40) at org.picocontainer.DefaultPicoContainer.getInstance(DefaultPicoContainer.java:698) at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:646) at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:631) at org.picocontainer.parameters.BasicComponentParameter$1.resolveInstance(BasicComponentParameter.java:118) at org.picocontainer.parameters.ComponentParameter$1.resolveInstance(ComponentParameter.java:136) at org.picocontainer.injectors.SingleMemberInjector.getParameter(SingleMemberInjector.java:78) at org.picocontainer.injectors.ConstructorInjector$CtorAndAdapters.getParameterArguments(ConstructorInjector.java:309) at org.picocontainer.injectors.ConstructorInjector$1.run(ConstructorInjector.java:335) at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:270) at org.picocontainer.injectors.ConstructorInjector.getComponentInstance(ConstructorInjector.java:364) at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64) at org.picocontainer.behaviors.Stored.getComponentInstance(Stored.java:91) at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64) at org.picocontainer.behaviors.Locked.getComponentInstance(Locked.java:40) at org.picocontainer.DefaultPicoContainer.getInstance(DefaultPicoContainer.java:698) at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:646) at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:677) at com.atlassian.jira.component.pico.CachingMutablePicoContainer.getComponent(CachingMutablePicoContainer.java:139) at com.atlassian.jira.component.pico.ComponentContainer.getComponent(ComponentContainer.java:555) at com.atlassian.jira.component.pico.ComponentManager.lambda$maybeGetComponent$3(ComponentManager.java:474) at java.util.Optional.map(Optional.java:215) at com.atlassian.jira.component.pico.ComponentManager.maybeGetComponent(ComponentManager.java:474) at com.atlassian.jira.component.pico.ComponentManager.getComponent(ComponentManager.java:462) at com.atlassian.jira.component.pico.ComponentManager.loadPluginSystemEventListeners(ComponentManager.java:277) at com.atlassian.jira.component.pico.ComponentManager.earlyStartPluginSystem(ComponentManager.java:237) at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:45) at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$2(DefaultJiraLauncher.java:145) at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:301) at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:196) at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:137) at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$0(DefaultJiraLauncher.java:104) at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31) at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:102) at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:154) at java.lang.Thread.run(Thread.java:748) Caused by: java.io.IOException: Failed to list contents of /var/atlassian/application-data/jira/plugins/.osgi-plugins/felix/felix-cache at org.apache.commons.io.FileUtils.verifiedListFiles(FileUtils.java:1751) at org.apache.commons.io.FileUtils.cleanDirectory(FileUtils.java:1716) at org.apache.commons.io.FileUtils.deleteDirectory(FileUtils.java:1617) at org.apache.commons.io.FileUtils.forceDelete(FileUtils.java:2391) at org.apache.commons.io.FileUtils.cleanDirectory(FileUtils.java:1721) ... 77 more 2022-08-10 14:00:09,097 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.
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 = , (Event: Level = (EventLevel: error) , Key = (EventType: setup) , Desc = Tomcat is misconfigured , Exception = The server.xml file is missing parameters needed by Jira to handle requests that contain special characters.
)] 2022-08-10 14:00:09,108 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage: --------------------------------------------------------------------------------- Heap memory : Used: 434 MiB. Committed: 5291 MiB. Max: 8022 MiB Non-heap memory : Used: 82 MiB. Committed: 98 MiB. Max: 1536 MiB --------------------------------------------------------------------------------- TOTAL : Used: 516 MiB. Committed: 5389 MiB. Max: 9558 MiB --------------------------------------------------------------------------------- Running ./start-jira.sh Atlassian Jira Version : 8.5.1 If you encounter issues starting or stopping JIRA, please see the Troubleshooting guide at https://docs.atlassian.com/jira/jadm-docs-085/Troubleshooting+installation 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 Tomcat started. Running sudo systemctl start jira $ sudo systemctl start jira Job for jira.service failed because the control process exited with error code. See "systemctl status jira.service" and "journalctl -xe" for detail $ sudo systemctl status jira ● jira.service - Atlassian Jira Loaded: loaded (/etc/systemd/system/jira.service; enabled; vendor preset: enabled) Active: failed (Result: exit-code) since Wed 2022-08-10 14:07:32 PDT; 53s ago Process: 10003 ExecStart=/opt/atlassian/jira/bin/start-jira.sh (code=exited, status=1/FAILURE) Main PID: 7936 (code=exited, status=0/SUCCESS) Aug 10 14:07:32 spartacus start-jira.sh[10003]: If you encounter issues starting or stopping JIRA, please see the Troubleshoo Aug 10 14:07:32 spartacus start-jira.sh[10003]: Server startup logs are located in /opt/atlassian/jira/logs/catalina.out Aug 10 14:07:32 spartacus start-jira.sh[10003]: Existing PID file found during start. Aug 10 14:07:32 spartacus start-jira.sh[10003]: Tomcat appears to still be running with PID 6947. Start aborted. Aug 10 14:07:32 spartacus start-jira.sh[10003]: If the following process is not a Tomcat process, remove the PID file and try Aug 10 14:07:32 spartacus start-jira.sh[10003]: UID PID PPID C STIME TTY TIME CMD Aug 10 14:07:32 spartacus start-jira.sh[10003]: jira 6947 1 8 13:59 pts/0 00:00:40 /opt/atlassian/jira/jre//bin/ Aug 10 14:07:32 spartacus systemd[1]: jira.service: Control process exited, code=exited status=1 Aug 10 14:07:32 spartacus systemd[1]: jira.service: Failed with result 'exit-code'. Aug 10 14:07:32 spartacus systemd[1]: Failed to start Atlassian Jira.

Dave Theodore [Coyote Creek Consulting] · Answer

Sounds like file system permissions to me.  Hopefully you get lucky and someone just started Jira as root user, and you just need to chown things back to the user Jira runs as.  Make sure selinux is not enforcing, and ensure that the user that Jira is running as has write permission to the indicated directory.

/var/atlassian/application-data/jira/plugins/.osgi-plugins/felix