Database: JIRA couldn't connect to your database

[injunhan]

jira worked well before, but it is failed to start jira service from this morning.

following is atlassian-jira.log (never changed dbconfig.xml, any server configuration)

2020-04-28 09:20:50,791 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/application-data/jira/dbconfig.xml
2020-04-28 09:20:50,852 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Trying to get encrypted password from xml and decrypt it
2020-04-28 09:20:50,853 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Database password decryption not performed.
2020-04-28 09:20:55,970 JIRA-Bootstrap ERROR [c.a.config.bootstrap.DefaultAtlassianBootstrapManager] Could not successfully test your database:
org.h2.jdbc.JdbcSQLException: General error: "java.lang.IllegalStateException: Reading from cache:nio:/var/atlassian/application-data/jira/database/h2db.mv.db failed; file length 84414464 read length 768 at 84414629 [1.4.185/1]" [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.<init>(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.<init>(JdbcConnection.java:108)
at org.h2.jdbc.JdbcConnection.<init>(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:219)
at com.atlassian.jira.config.database.DatabaseConfig.testConnection(DatabaseConfig.java:88)
at com.atlassian.jira.health.checks.DbConfigurationAndConnectionCheck.doPerform(DbConfigurationAndConnectionCheck.java:60)
at com.atlassian.jira.health.HealthCheckTemplate.perform(HealthCheckTemplate.java:23)
at com.atlassian.jira.health.DefaultHealthCheckExecutor.runCheck(DefaultHealthCheckExecutor.java:74)
at com.atlassian.jira.health.DefaultHealthCheckExecutor.lambda$applyAndCollectExceptions$1(DefaultHealthCheckExecutor.java:53)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at com.atlassian.jira.health.DefaultHealthCheckExecutor.applyAndCollectExceptions(DefaultHealthCheckExecutor.java:53)
at com.atlassian.jira.health.DefaultHealthCheckExecutor.performHealthChecks(DefaultHealthCheckExecutor.java:42)
at com.atlassian.jira.health.HealthChecks.executeChecksAndRecordResults(HealthChecks.java:164)
at com.atlassian.jira.health.HealthChecks.runHealthChecks(HealthChecks.java:154)
at com.atlassian.jira.health.HealthChecks.runHealthChecks(HealthChecks.java:66)
at com.atlassian.jira.startup.BootstrapContainerLauncher.start(BootstrapContainerLauncher.java:48)
at com.atlassian.jira.startup.DefaultJiraLauncher.preDbLaunch(DefaultJiraLauncher.java:117)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$0(DefaultJiraLauncher.java:103)
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.IllegalStateException: Reading from cache:nio:/var/atlassian/application-data/jira/database/h2db.mv.db failed; file length 84414464 read length 768 at 84414629 [1.4.185/1]
at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:773)
at org.h2.mvstore.DataUtils.readFully(DataUtils.java:443)
at org.h2.mvstore.FileStore.readFully(FileStore.java:98)
at org.h2.mvstore.Page.read(Page.java:189)
at org.h2.mvstore.MVStore.readPage(MVStore.java:1830)
at org.h2.mvstore.MVMap.setRootPos(MVMap.java:746)
at org.h2.mvstore.MVStore.openMap(MVStore.java:475)
at org.h2.mvstore.MVStore.openMap(MVStore.java:426)
at org.h2.store.LobStorageMap.init(LobStorageMap.java:93)
at org.h2.engine.Database.open(Database.java:761)
at org.h2.engine.Database.openDatabase(Database.java:266)
... 41 more
Caused by: java.io.EOFException
at org.h2.mvstore.DataUtils.readFully(DataUtils.java:431)
... 51 more
2020-04-28 09:20:56,012 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] JIRA couldn't connect to your database
2020-04-28 09:20:56,012 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.

2020-04-28 09:20:56,014 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] Running JIRA startup checks.
2020-04-28 09:20:56,014 JIRA-Bootstrap FATAL [c.a.jira.startup.JiraStartupLogger] Startup check failed. JIRA will be locked.
2020-04-28 09:20:56,115 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 84 MiB. Committed: 371 MiB. Max: 1980 MiB
Non-heap memory : Used: 46 MiB. Committed: 69 MiB. Max: 1536 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 130 MiB. Committed: 440 MiB. Max: 3516 MiB
---------------------------------------------------------------------------------

Please advise me.

thanks,

Injun.

[Daniel Ebers]

Hi Injun,

from browsing Atlassian Community with this specific error message it is likely that the H2 database became corrupted/crashed somehow.

It is advised to setup Jira on a supported database, f.e. PostgreSQL or MySQL.

In case you have a backup of the H2 database you could give it a try. Most likely it would make much sense to re-install the instance on a supported database assuming this was a test/non-production instance.

Cheers,
Daniel