Jira cannot start after server reboot

[Bartosz Kwapisz]

After server reboot, without any modification regarding jira, jira cannot start.
What could be the cause of the problem?
We don't know how to fix it and any help would be useful!

Some additional information:

•  Jira version: 8.19.0#819000-sha1:47bbf34f7e2d88d8af7d579f0393cc03c448e7ba
• JDK: OpenJDK Runtime Environment 11.0.11+9
• OS: Debian GNU/Linux 11 (bullseye)

Here is the first error in our log that we found (there are many such entries):

2022-10-14 22:30:24,993+0200 http-nio-18080-exec-1 ERROR anonymous 1350x1x1 - 127.0.0.1 / [c.atlassian.instrumentation.Instrument] Unable to snapshot thread local operations (implementation of OpTimerFactory is not a ThreadLocalOpTimerFactory): null
2022-10-14 22:30:25,043+0200 http-nio-18080-exec-2 WARN anonymous 1350x2x1 - 127.0.0.1 /secure/johnson/data [c.a.jira.security.JiraSecurityFilter] Rejecting security-sensitive request that bypassed Johnson filter: /jira/secure/johnson/data
2022-10-14 22:30:27,035+0200 FelixStartLevel WARN [o.e.g.b.e.internal.support.ExtenderConfiguration] Gemini Blueprint extensions bundle not present, annotation processing disabled.
2022-10-14 22:30:30,618+0200 ThreadPoolAsyncTaskExecutor::Thread 9 ERROR [c.a.p.osgi.factory.OsgiPlugin] Unable to start the plugin container for plugin 'com.atlassian.cluster.monitoring.cluster-monitoring-plugin'
org.springframework.beans.factory.BeanDefinitionStoreException: Unexpected exception parsing XML document from URL [bundle://34.0:0/META-INF/spring/context.xml]; nested exception is java.lang.IllegalStateException: Cannot execute atlassian-spring-scanner-runtime: plugin has an extra copy of atlassian-spring-scanner-annotation classes, perhaps embedded inside the target plugin 'com.atlassian.cluster.monitoring.cluster-monitoring-plugin'; embedding scanner-annotations is not supported since scanner version 2.0. Use 'mvn dependency:tree' and ensure the atlassian-spring-scanner-annotation dependency in your plugin has <scope>provided</scope>, not 'runtime' or 'compile', and you have NO dependency on atlassian-spring-scanner-runtime.
at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:420)
at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:337)
at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:305)
at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:188)
at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:224)
at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:195)
at org.eclipse.gemini.blueprint.context.support.OsgiBundleXmlApplicationContext.loadBeanDefinitions(OsgiBundleXmlApplicationContext.java:171)
at org.eclipse.gemini.blueprint.context.support.OsgiBundleXmlApplicationContext.loadBeanDefinitions(OsgiBundleXmlApplicationContext.java:141)
at org.springframework.context.support.AbstractRefreshableApplicationContext.refreshBeanFactory(AbstractRefreshableApplicationContext.java:130)
at org.springframework.context.support.AbstractApplicationContext.obtainFreshBeanFactory(AbstractApplicationContext.java:637)
at org.eclipse.gemini.blueprint.context.support.AbstractDelegatedExecutionApplicationContext.access$800(AbstractDelegatedExecutionApplicationContext.java:57)
at org.eclipse.gemini.blueprint.context.support.AbstractDelegatedExecutionApplicationContext$3.run(AbstractDelegatedExecutionApplicationContext.java:239)
at org.eclipse.gemini.blueprint.util.internal.PrivilegedUtils.executeWithCustomTCCL(PrivilegedUtils.java:85)
at org.eclipse.gemini.blueprint.context.support.AbstractDelegatedExecutionApplicationContext.startRefresh(AbstractDelegatedExecutionApplicationContext.java:217)
at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.stageOne(DependencyWaiterApplicationContextExecutor.java:224)
at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.refresh(DependencyWaiterApplicationContextExecutor.java:177)
at org.eclipse.gemini.blueprint.context.support.AbstractDelegatedExecutionApplicationContext.refresh(AbstractDelegatedExecutionApplicationContext.java:154)
at org.eclipse.gemini.blueprint.extender.internal.activator.LifecycleManager$1.run(LifecycleManager.java:213)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.lang.IllegalStateException: Cannot execute atlassian-spring-scanner-runtime: plugin has an extra copy of atlassian-spring-scanner-annotation classes, perhaps embedded inside the target plugin 'com.atlassian.cluster.monitoring.cluster-monitoring-plugin'; embedding scanner-annotations is not supported since scanner version 2.0. Use 'mvn dependency:tree' and ensure the atlassian-spring-scanner-annotation dependency in your plugin has <scope>provided</scope>, not 'runtime' or 'compile', and you have NO dependency on atlassian-spring-scanner-runtime.
at com.atlassian.plugin.spring.scanner.runtime.impl.AtlassianScannerBeanDefinitionParser.checkScannerRuntimeIsNotEmbeddedInBundle(AtlassianScannerBeanDefinitionParser.java:198)
at com.atlassian.plugin.spring.scanner.runtime.impl.AtlassianScannerBeanDefinitionParser.parse(AtlassianScannerBeanDefinitionParser.java:60)
at org.springframework.beans.factory.xml.NamespaceHandlerSupport.parse(NamespaceHandlerSupport.java:74)
at org.springframework.beans.factory.xml.BeanDefinitionParserDelegate.parseCustomElement(BeanDefinitionParserDelegate.java:1391)
at org.springframework.beans.factory.xml.BeanDefinitionParserDelegate.parseCustomElement(BeanDefinitionParserDelegate.java:1371)
at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.doRegisterBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:149)
at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.registerBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:96)
at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.registerBeanDefinitions(XmlBeanDefinitionReader.java:514)
at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:394)
... 20 more
2022-10-14 22:30:30,631+0200 ThreadPoolAsyncTaskExecutor::Thread 9 ERROR [o.e.g.b.e.internal.support.ExtenderConfiguration] Application context refresh failed (NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.cluster.monitoring.cluster-monitoring-plugin, config=osgibundle:/META-INF/spring/*.xml))
o

 And finally we see many timeouts like this:

2022-10-14 22:35:30,646+0200 Spring DM Context Creation Timer ERROR [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.diagnostics.atlassian-diagnostics-plugin' never resolved service '&diagnosticsConfiguration' with filter '(objectClass=com.atlassian.diagnostics.DiagnosticsConfiguration)'
2022-10-14 22:35:30,646+0200 Spring DM Context Creation Timer ERROR [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.diagnostics.atlassian-diagnostics-plugin' never resolved service '&monitoringService' with filter '(objectClass=com.atlassian.diagnostics.MonitoringService)'
2022-10-14 22:35:30,646+0200 Spring DM Context Creation Timer ERROR [c.a.p.osgi.factory.OsgiPlugin] Unable to start the plugin container for plugin 'com.atlassian.diagnostics.atlassian-diagnostics-plugin'
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.diagnostics.atlassian-diagnostics-plugin' has timed out waiting for (|(objectClass=com.atlassian.diagnostics.MonitoringService)(objectClass=com.atlassian.diagnostics.DiagnosticsConfiguration))
at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
at java.base/java.util.TimerThread.mainLoop(Unknown Source)
at java.base/java.util.TimerThread.run(Unknown Source)

[Brant Schroeder]

@Bartosz Kwapisz Welcome to the Atlassian community

Looks like a plugin issue.  I would suggest reviewing the following articles:

• https://confluence.atlassian.com/jirakb/troubleshoot-a-jira-server-startup-failed-error-394464512.html 
• https://confluence.atlassian.com/jirakb/jira-startup-fails-with-message-that-required-plugins-are-not-started-254738702.html 
• https://confluence.atlassian.com/confkb/plugins-are-disabled-at-startup-and-various-timeout-errors-appear-in-the-logs-after-startup-211651219.html 

I am thinking that the third article will resolve the issue.