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Updateing from 7.13.4 to 7.19.9 fails

Marc Stirner
Marc Stirner
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June 16, 2023

After installing/updating with the provided installer, the confluence server dosnt start and now http requests are proceeded.

 

/opt/confluence/application-data/logs/atlassian-confluence.log

```

2023-06-16 11:14:02,555 WARN [Catalina-utility-1] [plugin.osgi.util.OsgiHeaderUtil] stripDuplicatePackages removing duplicate import package com.atlassian.confluence.api.service.network~ for plugin com.atlassian.streams.confluence - it is likely that a duplicate package was supplied in the OSGi instructions in the plugin's MANIFEST.MF
2023-06-16 11:14:36,109 WARN [ThreadPoolAsyncTaskExecutor::Thread 8] [scanner.runtime.impl.ComponentImportBeanFactoryPostProcessor] loadServiceClass Unable to load class 'com.atlassian.jira.user.UserKeyService' for component importation purposes. Skipping...
2023-06-16 11:14:36,111 WARN [ThreadPoolAsyncTaskExecutor::Thread 8] [scanner.runtime.impl.ComponentImportBeanFactoryPostProcessor] loadServiceClass Unable to load class 'com.atlassian.jira.util.I18nHelper' for component importation purposes. Skipping...
2023-06-16 11:14:38,084 ERROR [ThreadPoolAsyncTaskExecutor::Thread 9] [internal.dependencies.startup.DependencyWaiterApplicationContextExecutor] logWrongState Expecting state (RESOLVING_DEPENDENCIES) not (DEPENDENCIES_RESOLVED) for context [NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.confluence.plugins.confluence-mobile, config=osgibundle:/META-INF/spring/*.xml)]; assuming an interruption and bailing out
2023-06-16 11:14:46,900 INFO [Catalina-utility-1] [atlassian.plugin.manager.DefaultPluginManager] logTime Plugin system earlyStartup ended
2023-06-16 11:14:46,936 WARN [AtlassianEvent::CustomizableThreadFactory-4] [core.persistence.hibernate.HibernateVersionHistoryDao] getLatestBuildNumber Unable to determine build number from database. If you are upgrading from a Confluence version prior to 7.14.0, this is expected: Unknown column 'FINALIZED' in 'where clause'
2023-06-16 11:14:47,122 INFO [Catalina-utility-1] [confluence.upgrade.impl.DefaultUpgradeManager] beforeUpgrade Generating pre-upgrade recovery file...
2023-06-16 11:14:47,151 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] begin Starting
2023-06-16 11:14:47,156 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] logTask Starting DATABASE_INFORMATION
2023-06-16 11:14:47,161 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] logTask Finishing DATABASE_INFORMATION
2023-06-16 11:14:47,161 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] logTask Starting TABLE_DEFINITION
2023-06-16 11:14:47,664 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] logTask Finishing TABLE_DEFINITION
2023-06-16 11:14:47,665 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] totalNumberOfTables Total number of tables: 224
2023-06-16 11:14:47,665 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] logTask Starting TABLES_DATA

 

 

 

 

 


2023-06-16 11:17:30,495 WARN [Catalina-utility-1] [confluence.impl.hibernate.ConfluenceHibernateTransactionManager] doRollback Performing rollback. Transactions:
->[null]: PROPAGATION_REQUIRES_NEW,ISOLATION_DEFAULT (Session #835469687)
2023-06-16 11:17:30,538 ERROR [Catalina-utility-1] [springframework.transaction.support.TransactionTemplate] rollbackOnException Application exception overridden by rollback exception
java.lang.OutOfMemoryError: Java heap space
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3515)
at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:2088)
at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1992)
at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:3413)
at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:471)
at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:3115)
at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:2344)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2739)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2491)
at com.mysql.jdbc.ConnectionImpl.setAutoCommit(ConnectionImpl.java:4807)
at com.mchange.v2.c3p0.impl.NewProxyConnection.setAutoCommit(NewProxyConnection.java:1059)
at com.atlassian.config.db.DelegatingConnection.setAutoCommit(DelegatingConnection.java:53)
at jdk.internal.reflect.GeneratedMethodAccessor299.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.atlassian.activeobjects.spi.ConnectionHandler.delegate(ConnectionHandler.java:39)
at com.atlassian.activeobjects.spi.ConnectionHandler.invoke(ConnectionHandler.java:34)
at com.sun.proxy.$Proxy2468.setAutoCommit(Unknown Source)
at com.atlassian.dbexporter.jdbc.JdbcUtils.withNoAutoCommit(JdbcUtils.java:54)
at com.atlassian.dbexporter.exporter.DataExporter.lambda$export$1(DataExporter.java:50)
at com.atlassian.dbexporter.exporter.DataExporter$$Lambda$1933/0x000000080215ac40.call(Unknown Source)
at com.atlassian.dbexporter.jdbc.JdbcUtils.withConnection(JdbcUtils.java:29)
at com.atlassian.dbexporter.exporter.DataExporter.export(DataExporter.java:48)
at com.atlassian.dbexporter.DbExporter.exportData(DbExporter.java:65)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.lambda$generate$0(DefaultRecoveryFileGenerator.java:80)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator$$Lambda$1914/0x0000000802147440.doInTransaction(Unknown Source)
at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:140)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.generate(DefaultRecoveryFileGenerator.java:61)
at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.beforeUpgrade(DefaultUpgradeManager.java:173)
at com.atlassian.confluence.upgrade.AbstractUpgradeManager.upgrade(AbstractUpgradeManager.java:134)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.launchUpgrades(PluginFrameworkContextListener.java:122)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.contextInitialized(PluginFrameworkContextListener.java:82)
2023-06-16 11:17:30,539 ERROR [Catalina-utility-1] [atlassian.confluence.plugin.PluginFrameworkContextListener] contextInitialized Error initialising plugin manager: Could not roll back Hibernate transaction; nested exception is net.sf.hibernate.TransactionException: Unable to rollback against JDBC Connection
org.springframework.transaction.TransactionSystemException: Could not roll back Hibernate transaction; nested exception is net.sf.hibernate.TransactionException: Unable to rollback against JDBC Connection
at org.springframework.orm.hibernate.HibernateTransactionManager.doRollback(HibernateTransactionManager.java:535)
at com.atlassian.confluence.impl.hibernate.ConfluenceHibernateTransactionManager.doRollback(ConfluenceHibernateTransactionManager.java:81)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.processRollback(AbstractPlatformTransactionManager.java:835)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.rollback(AbstractPlatformTransactionManager.java:809)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
at com.sun.proxy.$Proxy79.rollback(Unknown Source)
at org.springframework.transaction.support.TransactionTemplate.rollbackOnException(TransactionTemplate.java:168)
at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:144)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.generate(DefaultRecoveryFileGenerator.java:61)
at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.beforeUpgrade(DefaultUpgradeManager.java:173)
at com.atlassian.confluence.upgrade.AbstractUpgradeManager.upgrade(AbstractUpgradeManager.java:134)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.launchUpgrades(PluginFrameworkContextListener.java:122)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.contextInitialized(PluginFrameworkContextListener.java:82)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4491)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4939)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1332)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1322)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: net.sf.hibernate.TransactionException: Unable to rollback against JDBC Connection
at org.hibernate.resource.jdbc.internal.AbstractLogicalConnectionImplementor.rollback(AbstractLogicalConnectionImplementor.java:122)
at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcResourceLocalTransactionCoordinatorImpl$TransactionDriverControlImpl.rollback(JdbcResourceLocalTransactionCoordinatorImpl.java:251)
at org.hibernate.engine.transaction.internal.TransactionImpl.rollback(TransactionImpl.java:100)
at com.atlassian.hibernate.adapter.adapters.TransactionV2Adapter.rollback(TransactionV2Adapter.java:44)
at org.springframework.orm.hibernate.HibernateTransactionManager.doRollback(HibernateTransactionManager.java:532)
... 28 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed.
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.base/java.lang.reflect.Constructor.newInstance(Unknown Source)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
at com.mysql.jdbc.Util.getInstance(Util.java:408)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:919)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:898)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:887)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:861)
at com.mysql.jdbc.ConnectionImpl.throwConnectionClosedException(ConnectionImpl.java:1192)
at com.mysql.jdbc.ConnectionImpl.checkClosed(ConnectionImpl.java:1187)
at com.mysql.jdbc.ConnectionImpl.rollback(ConnectionImpl.java:4534)
at com.mchange.v2.c3p0.impl.NewProxyConnection.rollback(NewProxyConnection.java:1033)
at org.hibernate.resource.jdbc.internal.AbstractLogicalConnectionImplementor.rollback(AbstractLogicalConnectionImplementor.java:116)
... 32 more
Caused by: java.lang.OutOfMemoryError: Java heap space
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3515)
at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:2088)
at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1992)
at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:3413)
at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:471)
at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:3115)
at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:2344)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2739)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2491)
at com.mysql.jdbc.ConnectionImpl.setAutoCommit(ConnectionImpl.java:4807)
at com.mchange.v2.c3p0.impl.NewProxyConnection.setAutoCommit(NewProxyConnection.java:1059)
at com.atlassian.config.db.DelegatingConnection.setAutoCommit(DelegatingConnection.java:53)
at jdk.internal.reflect.GeneratedMethodAccessor299.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.atlassian.activeobjects.spi.ConnectionHandler.delegate(ConnectionHandler.java:39)
at com.atlassian.activeobjects.spi.ConnectionHandler.invoke(ConnectionHandler.java:34)
at com.sun.proxy.$Proxy2468.setAutoCommit(Unknown Source)
at com.atlassian.dbexporter.jdbc.JdbcUtils.withNoAutoCommit(JdbcUtils.java:54)
at com.atlassian.dbexporter.exporter.DataExporter.lambda$export$1(DataExporter.java:50)
at com.atlassian.dbexporter.exporter.DataExporter$$Lambda$1933/0x000000080215ac40.call(Unknown Source)
at com.atlassian.dbexporter.jdbc.JdbcUtils.withConnection(JdbcUtils.java:29)
at com.atlassian.dbexporter.exporter.DataExporter.export(DataExporter.java:48)
at com.atlassian.dbexporter.DbExporter.exportData(DbExporter.java:65)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.lambda$generate$0(DefaultRecoveryFileGenerator.java:80)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator$$Lambda$1914/0x0000000802147440.doInTransaction(Unknown Source)
at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:140)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.generate(DefaultRecoveryFileGenerator.java:61)
at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.beforeUpgrade(DefaultUpgradeManager.java:173)
at com.atlassian.confluence.upgrade.AbstractUpgradeManager.upgrade(AbstractUpgradeManager.java:134)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.launchUpgrades(PluginFrameworkContextListener.java:122)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.contextInitialized(PluginFrameworkContextListener.java:82)
2023-06-16 11:17:30,602 INFO [Catalina-utility-1] [confluence.upgrade.impl.DefaultUpgradeGate] waitForBooleanValue Waiting to find if plugin dependent upgrades are required. Maximum wait time will be 90 seconds.
2023-06-16 11:17:30,604 INFO [Catalina-utility-1] [confluence.upgrade.impl.DefaultUpgradeGate] waitForBooleanValue plugin dependent upgrades are required : true.
2023-06-16 11:17:30,609 INFO [Catalina-utility-1] [confluence.upgrade.impl.DefaultUpgradeGate] waitForBooleanValue Waiting to find if plugin dependent upgrades are complete. Maximum wait time will be 1800 seconds.

```

 

 

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Tyrell Bobowski
Tyrell Bobowski
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November 5, 2023

I ran into the same issue trying to upgrade from 7.13.0 to 7.19.16.  I was able to get the upgrade to complete by doing the following.

After running the upgrade it failed and I could see Java Out of Memory errors in the atlassian-confluence.log file so I increased the Java Heap size to 2GB
/opt/atlassian/confluence/bin/setenv.sh
CATALINA_OPTS="-Xms2048m -Xmx2048m ${CATALINA_OPTS}"
***Note I originally did this before running the upgrade but after the upgrade was started it overwrote this file and set it back to 1GB so I had to set it again
Restarted Confluence but still got the same error in your screenshot.  Atlassian-Confluence.log no longer shows the OutofMemory error but instead was showing lose of connection to the mysql database.  I stopped Confluence and then did this

  1. Remove Corrupt JAR Cache

    Delete the following plugin cache folders and restart Confluence:

    • <confluence-home>/bundled-plugins
    • <confluence-home>/plugins-cache
    • <confluence-home>/plugins-osgi-cache
    • confluence-home>/plugins-temp

https://confluence.atlassian.com/confkb/unable-to-start-up-confluence-372081272.html

Started Confluence again and the upgrade was now able to finish successfully and 7.19.16 was now working.




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Marc Stirner
Marc Stirner
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June 19, 2023

This is strange, since we had the memoy limit set to 12GB.
After playing around with it, and setting it to 4GB a error page can be viewed:

 Screenshot 2023-06-19 at 13-24-53 Errors.png

```
Could not roll back Hibernate transaction; nested exception is net.sf.hibernate.TransactionException: Unable to rollback against JDBC Connection
```

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