Running Jira Startup Check failed. Jira will be locked

Question

The memory in the VM (where Jira was installed) has been full due to which Jira failed to start up. I cleared the logs and started the Jira instance using ./start-jira.sh and getting the below error. There has been no change in the configuration settings. Jira Version 7.3.1 2018-03-05 17:15:57,455 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /root/JIRA/home/dbconfig.xml 2018-03-05 17:16:03,732 JIRA-Bootstrap ERROR [c.a.config.bootstrap.DefaultAtlassianBootstrapManager] Could not successfully test your database: org.h2.jdbc.JdbcSQLException: General error: "java.lang.IllegalStateException: The transaction log might be corrupt for key 124472 [1.4.185/100]" [50000-185] at org.h2.message.DbException.getJdbcSQLException(DbException.java:345) at org.h2.message.DbException.get(DbException.java:168) at org.h2.message.DbException.convert(DbException.java:295) at org.h2.engine.Database.openDatabase(Database.java:297) at org.h2.engine.Database.(Database.java:260) at org.h2.engine.Engine.openSession(Engine.java:60) at org.h2.engine.Engine.openSession(Engine.java:167) at org.h2.engine.Engine.createSessionAndValidate(Engine.java:145) at org.h2.engine.Engine.createSession(Engine.java:128) at org.h2.engine.Engine.createSession(Engine.java:26) at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:347) at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:108) at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:92) at org.h2.Driver.connect(Driver.java:72) at java.sql.DriverManager.getConnection(DriverManager.java:664) at java.sql.DriverManager.getConnection(DriverManager.java:247) at com.atlassian.config.bootstrap.DefaultAtlassianBootstrapManager.getTestDatabaseConnection(DefaultAtlassianBootstrapManager.java:347) at com.atlassian.jira.config.database.JdbcDatasource.getConnection(JdbcDatasource.java:211) Caused by: java.lang.IllegalStateException: The transaction log might be corrupt for key 124472 [1.4.185/100] at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:773) at org.h2.mvstore.db.TransactionStore$TransactionMap.getValue(TransactionStore.java:1224) at org.h2.mvstore.db.TransactionStore$TransactionMap.getValue(TransactionStore.java:1184) at org.h2.mvstore.db.TransactionStore$TransactionMap.get(TransactionStore.java:1161) at org.h2.mvstore.db.TransactionStore$TransactionMap.get(TransactionStore.java:1129) at org.h2.mvstore.db.MVPrimaryIndex.(MVPrimaryIndex.java:79) at org.h2.mvstore.db.MVTable.init(MVTable.java:90) at org.h2.mvstore.db.MVTableEngine.createTable(MVTableEngine.java:130) at org.h2.mvstore.db.MVTableEngine.createTable(MVTableEngine.java:41) at org.h2.schema.Schema.createTable(Schema.java:582) at org.h2.command.ddl.CreateTable.update(CreateTable.java:137) at org.h2.engine.MetaRecord.execute(MetaRecord.java:58) at org.h2.engine.Database.open(Database.java:732) at org.h2.engine.Database.openDatabase(Database.java:266) ... 41 more 2018-03-05 17:16:03,749 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] JIRA couldn't connect to your database 2018-03-05 17:16:03,749 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] JIRA failed to establish a connection to your database. This could be because: - Your database isn't running - The configuration of your dbconfig.xml file is incorrect (user, password, or database URL etc.) - There is a network issue between JIRA and your database (e.g. firewall, database doesn't allow remote access etc.) There are several other solutions you can try, review our documentation and see what works for you. 2018-03-05 17:16:03,753 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] Running JIRA startup checks. 2018-03-05 17:16:03,753 JIRA-Bootstrap FATAL [c.a.jira.startup.JiraStartupLogger] Startup check failed. JIRA will be locked. 2018-03-05 17:16:03,972 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage: --------------------------------------------------------------------------------- Heap memory : Used: 221 MiB. Committed: 489 MiB. Max: 745 MiB Non-heap memory : Used: 49 MiB. Committed: 50 MiB. Max: 1264 MiB --------------------------------------------------------------------------------- TOTAL : Used: 270 MiB. Committed: 539 MiB. Max: 2009 MiB ---------------------------------------------------------------------------------

Jamie Heutmaker · Answer

I have a similar problem running Jira 8.2.1 in Kubernetes. Logs look like this:

user.country : US
user.dir : /var/atlassian/application-data/jira
user.home : /home/jira
user.language : en
user.name : jira
user.timezone : America/Chicago

2019-09-24 14:33:21,909 localhost-startStop-1 INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/application-data/jira/dbconfig.xml
2019-09-24 14:33:22,162 localhost-startStop-1 INFO [c.a.jira.startup.JiraStartupLogger] Running JIRA startup checks.
2019-09-24 14:33:22,163 localhost-startStop-1 FATAL [c.a.jira.startup.JiraStartupLogger] Startup check failed. JIRA will be locked.
2019-09-24 14:33:22,213 localhost-startStop-1 INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 160 MiB. Committed: 990 MiB. Max: 3960 MiB
Non-heap memory : Used: 36 MiB. Committed: 61 MiB. Max: 1536 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 196 MiB. Committed: 1050 MiB. Max: 5496 MiB
---------------------------------------------------------------------------------
24-Sep-2019 14:33:22.426 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
24-Sep-2019 14:33:22.430 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
24-Sep-2019 14:33:22.443 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 5238 ms
24-Sep-2019 14:35:41.779 INFO [Thread-4] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
24-Sep-2019 14:35:41.785 INFO [Thread-4] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
2019-09-24 14:35:41,809 localhost-startStop-2 INFO [c.a.jira.startup.DefaultJiraLauncher] Stopping launchers24-Sep-2019 14:35:41.863 SEVERE [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.checkThreadLocalMapForLeaks The web application [ROOT] created a ThreadLocal with key of type [org.picocontainer.DefaultPicoContainer.IntoThreadLocal] (value [org.picocontainer.DefaultPicoContainer$IntoThreadLocal@4a1b9b3a]) and a value of type [java.lang.Class] (value [class org.picocontainer.ComponentAdapter$NOTHING]) 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. It repeats this last part several times. Just started happening. Same image fine in Dev environment. Fails in IT. Any ideas?

Laurens Coppens · Answer

Hi,

What database are you using?

The log says its probably database related.

Regards,

Laurens