Fresh install of Jira does not run - using MySQL Connector 5.1.49

[Daniel Webster]

Hello all,

As per subject, Jira is refusing to start, and stack traces. This is a fresh install with a clean database, and no artifacts from a previous instance.

We are using MySQL Connector 5.1.49, and the below has occurred with both MySQL and MariaDB RDS (AWS).

Any insights appreciated!

Cheers

Dan

2020-11-30 09:19:59,663+0000 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] Running Jira startup checks. [130/87448]
2020-11-30 09:19:59,663+0000 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] Jira pre-database startup checks completed successfully.
2020-11-30 09:20:22,892+0000 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigurationManagerImpl] The database is configured. Now running Database Chec
klist Launcher 
2020-11-30 09:20:22,900+0000 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseChecklistLauncher] Jira database startup checks completed successfully.
2020-11-30 09:20:22,901+0000 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigurationManagerImpl] The database is configured. Now running Post database
-configuration launchers 
2020-11-30 09:20:24,195+0000 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/a
pplication-data/jira/dbconfig.xml 
2020-11-30 09:20:24,198+0000 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Trying to get encrypted password from xml and decrypt it 
2020-11-30 09:20:24,198+0000 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Database password decryption not performed.
2020-11-30 09:20:27,153+0000 JIRA-Bootstrap INFO [c.a.jira.upgrade.PluginUpgradeListener] [plugin-upgrade-listener] Created 
2020-11-30 09:20:27,286+0000 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseLauncher] Database transactions enabled: true 
2020-11-30 09:20:27,287+0000 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseLauncher] Using JIRA's default for database transaction isolation level: 2 
2020-11-30 09:20:27,291+0000 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] 

Database configuration OK 

___ Database Configuration _________________ 

Loading entityengine.xml from : file:/opt/atlassian/jira/atlassian-jira/WEB-INF/classes/entityengine.xml 
Entity model field type name : mysql 
Entity model schema name : 
Database Version : MySQL - 5.5.5-10.4.13-MariaDB-log 
Database Driver : MySQL Connector Java - mysql-connector-java-5.1.49 ( Revision: ad86f36e100e104cd926c6b81c8cab9565750116 )
Database URL : jdbc:mysql://atlassian-jira.db.my.domain:3306/jira2?useUnicode=true&characterEncoding=UTF8&sessio
nVariables=default_storage_engine=InnoDB 
Database JDBC config : mysql jdbc:mysql://atlassian-jira.db.my.domain:3306/jira2?useUnicode=true&characterEncoding=UTF8&
sessionVariables=default_storage_engine=InnoDB 

2020-11-30 09:20:27,347+0000 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] 

___ Starting the JIRA Plugin System _________________

2020-11-30 09:20:30,259+0000 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. null 
at com.atlassian.jira.component.pico.ComponentManager$PluginSystem.earlyStartup(ComponentManager.java:676) 
at com.atlassian.jira.component.pico.ComponentManager.earlyStartPluginSystem(ComponentManager.java:238) 
at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:45) 
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$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$0(DefaultJiraLauncher.java:104) 
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:102) 
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:154) 
at java.lang.Thread.run(Thread.java:748) 
Caused by: java.lang.NullPointerException 
at com.atlassian.plugin.osgi.container.felix.FelixOsgiContainerManager.addBundleListener(FelixOsgiContainerManager.java:460)
at com.atlassian.plugin.osgi.factory.OsgiBundlePlugin.installInternal(OsgiBundlePlugin.java:224) 
at com.atlassian.plugin.impl.AbstractPlugin.install(AbstractPlugin.java:369) 
at com.atlassian.plugin.manager.DefaultPluginManager.lambda$addPlugins$20(DefaultPluginManager.java:1178) 
at com.atlassian.plugin.manager.PluginTransactionContext.wrap(PluginTransactionContext.java:63) 
at com.atlassian.jira.plugin.JiraPluginManager.addPlugins(JiraPluginManager.java:157) 
at com.atlassian.plugin.manager.DefaultPluginManager.lambda$earlyStartup$3(DefaultPluginManager.java:588) 
at com.atlassian.plugin.manager.PluginTransactionContext.wrap(PluginTransactionContext.java:63) 
at com.atlassian.plugin.manager.DefaultPluginManager.earlyStartup(DefaultPluginManager.java:523) 
at com.atlassian.jira.plugin.JiraPluginManager.earlyStartup(JiraPluginManager.java:119) 
at com.atlassian.jira.component.pico.ComponentManager$PluginSystem.earlyStartup(ComponentManager.java:669) 
... 11 more 
2020-11-30 09:20:31,208+0000 JIRA-Bootstrap ERROR [c.a.jira.startup.DefaultJiraLauncher] JIRA has failed to start because of the following errors: [(Event: Lev
el = (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 o
n contacting our support team and creating a support zip.), (Event: Level = (EventLevel: fatal) , Key = (EventType: database) , Desc = Could not execute health che$
k, DatabaseConfigurationManager not available. , Exception = ] 
2020-11-30 09:20:31,212+0000 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Startup is complete. Jira is ready to serve.

[Daniel Webster · Accepted solution]

The answer to this is to downgrade the MySQL connector to 5.1.46.