Updateing from 7.13.4 to 7.19.9 fails

Marc Stirner
I'm New Here
I'm New Here
Those new to the Atlassian Community have posted less than three times. Give them a warm welcome!
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.

```

 

 

2 answers

0 votes
Tyrell Bobowski
I'm New Here
I'm New Here
Those new to the Atlassian Community have posted less than three times. Give them a warm welcome!
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.




0 votes
Mohamed Benziane
Community Leader
Community Leader
Community Leaders are connectors, ambassadors, and mentors. On the online community, they serve as thought leaders, product experts, and moderators.
June 16, 2023
Marc Stirner
I'm New Here
I'm New Here
Those new to the Atlassian Community have posted less than three times. Give them a warm welcome!
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
```

Suggest an answer

Log in or Sign up to answer
TAGS
AUG Leaders

Atlassian Community Events