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Issue upgrading confluence from CentOS 7 6.0.4 to Ubuntu 16.04 6.5.0 with Galera cluster.

Robert Jackson
Robert Jackson
Contributor
April 10, 2018

Hello all,

I am having some issues with upgrading my confluence server as previously stated. I am changing distributions as well although I don't think that this would cause an issue. One notable difference that I have this go around is that I am using a highly available MySQL 5.6 3 node cluster via Galera.

Screen-Shot-2018-04-11-at-12.47.12-AM.png

Hera is the corresponding log events for this:

2018-04-11 05:38:17,805 ERROR [Long running task: Importing data] [engine.jdbc.spi.SqlExceptionHelper] logExceptions No operations allowed after connection closed.
 -- url: /setup/longrunningtaskxml.action | traceId: 6a5a74143e20b185 | userName: anonymous | referer: http://grimoire.scriptmyjob.com/setup/setup-restore-progress.action?taskId=913b9549-4451-4f67-bc54-7f259ff156c9 | action: longrunningtaskxml
2018-04-11 05:38:17,829 WARN [Long running task: Importing data] [confluence.upgrade.impl.DefaultUpgradeManager] setDatabaseBuildNumber Unable to set build number '7502' in the database
 -- url: /setup/longrunningtaskxml.action | traceId: 6a5a74143e20b185 | userName: anonymous | referer: http://grimoire.scriptmyjob.com/setup/setup-restore-progress.action?taskId=913b9549-4451-4f67-bc54-7f259ff156c9 | action: longrunningtaskxml
org.springframework.dao.DataAccessResourceFailureException: could not prepare statement; nested exception is org.hibernate.exception.JDBCConnectionException: could not prepare statement
 at org.springframework.orm.hibernate5.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:220)
 at org.springframework.orm.hibernate5.HibernateTemplate.doExecute(HibernateTemplate.java:366)
 at org.springframework.orm.hibernate5.HibernateTemplate.executeWithNativeSession(HibernateTemplate.java:326)
 at org.springframework.orm.hibernate5.HibernateTemplate.findByNamedQueryAndNamedParam(HibernateTemplate.java:989)
 at org.springframework.orm.hibernate5.HibernateTemplate.findByNamedQueryAndNamedParam(HibernateTemplate.java:978)
 at com.atlassian.confluence.core.persistence.hibernate.HibernateVersionHistoryDao.getVersionHistory(HibernateVersionHistoryDao.java:44)
 at com.atlassian.confluence.core.persistence.hibernate.HibernateVersionHistoryDao.addBuildToHistory(HibernateVersionHistoryDao.java:116)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:498)
 at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
 at com.atlassian.spring.interceptors.SpringProfilingInterceptor.invoke(SpringProfilingInterceptor.java:16)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
 at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
 at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
 at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
 at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
 at com.sun.proxy.$Proxy161.addBuildToHistory(Unknown Source)
 at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.setDatabaseBuildNumber(DefaultUpgradeManager.java:200)
 at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.setDatabaseBuildNumber(DefaultUpgradeManager.java:187)
 at com.atlassian.confluence.importexport.xmlimport.BackupImporter.doUpgrades(BackupImporter.java:354)
 at com.atlassian.confluence.importexport.xmlimport.BackupImporter.doImportInternal(BackupImporter.java:229)
 at com.atlassian.confluence.importexport.Importer.doImport(Importer.java:73)
 at com.atlassian.confluence.importexport.DefaultImportExportManager.performImportInternal(DefaultImportExportManager.java:131)
 at com.atlassian.confluence.importexport.DefaultImportExportManager.doPerformImport(DefaultImportExportManager.java:119)
 at com.atlassian.confluence.importexport.DefaultImportExportManager.performImport(DefaultImportExportManager.java:114)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:498)
 at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
 at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
 at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
 at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
 at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
 at com.sun.proxy.$Proxy243.performImport(Unknown Source)
 at com.atlassian.confluence.importexport.actions.ImportLongRunningTask.runInternal(ImportLongRunningTask.java:74)
 at com.atlassian.confluence.util.longrunning.ConfluenceAbstractLongRunningTask.run(ConfluenceAbstractLongRunningTask.java:26)
 at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
 at com.atlassian.confluence.tenant.TenantGate$3.call(TenantGate.java:145)
 at com.atlassian.confluence.tenant.OpenTenantGateLongRunningTask.run(OpenTenantGateLongRunningTask.java:24)
 at com.atlassian.confluence.util.longrunning.ManagedTask.run(ManagedTask.java:52)
 at com.atlassian.confluence.impl.util.concurrent.ConfluenceExecutors$ThreadLocalContextTaskWrapper.lambda$wrap$1(ConfluenceExecutors.java:90)
 at com.atlassian.confluence.vcache.VCacheRequestContextOperations.lambda$doInRequestContext$0(VCacheRequestContextOperations.java:50)
 at com.atlassian.confluence.impl.vcache.VCacheRequestContextManager.doInRequestContextInternal(VCacheRequestContextManager.java:87)
 at com.atlassian.confluence.impl.vcache.VCacheRequestContextManager.doInRequestContext(VCacheRequestContextManager.java:71)
 at com.atlassian.confluence.vcache.VCacheRequestContextOperations.doInRequestContext(VCacheRequestContextOperations.java:49)
 at com.atlassian.confluence.vcache.VCacheRequestContextOperations.lambda$withRequestContext$2(VCacheRequestContextOperations.java:66)
 at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
 at java.util.concurrent.FutureTask.run(FutureTask.java:266)
 at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
 at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
 at java.lang.Thread.run(Thread.java:748)
Caused by: org.hibernate.exception.JDBCConnectionException: could not prepare statement
 at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:48)
 at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)
 at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:111)
 at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:182)
 at org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(StatementPreparerImpl.java:148)
 at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1940)
 at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1909)
 at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1887)
 at org.hibernate.loader.Loader.doQuery(Loader.java:932)
 at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:349)
 at org.hibernate.loader.Loader.doList(Loader.java:2615)
 at org.hibernate.loader.Loader.doList(Loader.java:2598)
 at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2430)
 at org.hibernate.loader.Loader.list(Loader.java:2425)
 at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:502)
 at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:370)
 at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:216)
 at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1481)
 at org.hibernate.query.internal.AbstractProducedQuery.doList(AbstractProducedQuery.java:1441)
 at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1410)
 at org.springframework.orm.hibernate5.HibernateTemplate$33.doInHibernate(HibernateTemplate.java:1001)
 at org.springframework.orm.hibernate5.HibernateTemplate$33.doInHibernate(HibernateTemplate.java:989)
 at org.springframework.orm.hibernate5.HibernateTemplate.doExecute(HibernateTemplate.java:359)
 ... 58 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed.
 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
 at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
 at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
 at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
 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:1184)
 at com.mysql.jdbc.ConnectionImpl.checkClosed(ConnectionImpl.java:1179)
 at com.mysql.jdbc.ConnectionImpl.prepareStatement(ConnectionImpl.java:4071)
 at com.mysql.jdbc.ConnectionImpl.prepareStatement(ConnectionImpl.java:4040)
 at com.mchange.v2.c3p0.impl.NewProxyConnection.prepareStatement(NewProxyConnection.java:387)
 at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(StatementPreparerImpl.java:146)
 at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:172)
 ... 77 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

The last packet successfully received from the server was 145,197 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
 at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
 at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
 at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
 at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
 at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:990)
 at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3559)
 at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3459)
 at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3900)
 at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
 at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
 at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2480)
 at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2438)
 at com.mysql.jdbc.StatementImpl.executeQuery(StatementImpl.java:1381)
 at com.mchange.v2.c3p0.impl.NewProxyStatement.executeQuery(NewProxyStatement.java:327)
 at com.atlassian.confluence.core.persistence.hibernate.HibernateVersionHistoryDao.getLatestBuildNumber(HibernateVersionHistoryDao.java:30)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:498)
 at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
 at com.atlassian.spring.interceptors.SpringProfilingInterceptor.invoke(SpringProfilingInterceptor.java:16)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
 at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
 at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
 at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
 at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
 at com.sun.proxy.$Proxy161.getLatestBuildNumber(Unknown Source)
 at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.setDatabaseBuildNumber(DefaultUpgradeManager.java:197)
 ... 37 more
Caused by: java.io.EOFException: Can not read response from server. Expected to read 4 bytes, read 0 bytes before connection was unexpectedly lost.
 at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:3011)
 at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3469)
 ... 62 more

Here is my Infrastructure as code for standing up the Galera Cluster:
https://github.com/ScriptMyJob/Galera_Cluster

And here is my IaC for the Confluence App server:
https://github.com/ScriptMyJob/Grimoire

Any help would be very much appreciated.

Repsectfully,
Robert J.

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Shannon S
Shannon S
Atlassian Team
Atlassian Team members are employees working across the company in a wide variety of roles.
April 11, 2018

Robert,

Which version of MySQL 5.6 are you using? Note that you cannot use any versions earlier than 5.6.16 per our Supported Platforms.

The errors you're encountering look much like those documented in this article:

Regards,
Shannon

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Robert Jackson
Robert Jackson
Contributor
April 11, 2018

Shannon,

Thank you for reaching out about this.  I am using MySQL 5.6.39 with Galera Replication:

# mysql --version
mysql Ver 14.14 Distrib 5.6.39, for Linux (x86_64) using EditLine wrapper
# mysql
...
Server version: 5.6.39 MySQL Wsrep Server (GPL), wsrep_25.22
...

Has anyone attempted to configure Confluence using MySQL with Galera?  High availability is important to me hence why I am performing master-master replication.  Ideally, I would just use an RDS instance but I would be unable to make the Confluence optimizations found here:

https://confluence.atlassian.com/doc/database-setup-for-mysql-128747.html

At this point, I am willing to try anything.  Do you have any recommendations on how I can configure MySQL with master-master replication to work with confluence?

Respectfully,

Robert J.

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Shannon S
Shannon S
Atlassian Team
Atlassian Team members are employees working across the company in a wide variety of roles.
April 11, 2018

Robert,

That I don't know, as I'm not very familiar with Galera and haven't spoken to any customers trying to set it up.

I did find a few things, however:

Can you confirm that you went through the article I sent earlier?

Regards,

Shannon

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Robert Jackson
Robert Jackson
Contributor
April 11, 2018

Shannon,

Thanks for reaching back about this.  I did read over the articles that you sent earlier and will look into the new several nines article that you just sent when I have time this evening.

Thank you very much for your time.  I will update this ticket with my findings.

Respectfully,

Robert J.

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