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how to confluence update from 5.1.3 to 6.2-6.4

xingmiao
xingmiao September 26, 2017

Hello, I update confluence from 5.1.3 to 6.2-6.4 . My server 5.1.3  has many spaces, a lot of data . I refer to  the offical document https://confluence.atlassian.com/doc/upgrading-confluence-manually-255363437.html  to update my server,but I faild .

My  operating steps as follows:

1、Manage Add-ons ——Enable Safe Mode ——confluence Update check——select the version which I want to update ——Check——Disabled。

2、stop confluence server 5.1.3

3、sh atlassian-confluence-6.4.0-x64.bin

4、select update and overwrite the confluence home directory，backup data 

5、modify  confluence installed directory  file bin/setenv.sh . Modify CATALINA_OPTS="-Xms1024m -Xmx1024m -XX:+UseG1GC ${CATALINA_OPTS}" to CATALINA_OPTS="-Xms2048m -Xmx2048m -XX:+UseG1GC ${CATALINA_OPTS}"

6、jdk=1.8.0_91

     JAVA_OPTS="-server -Xms4096m -Xmx4096m -XX:MaxPermSize=1024m -XX:+UseG1GC"

7、confluence start but failed. The log is 

26-Sep-2017 17:51:22.968 INFO [localhost-startStop-2] org.springframework.context.support.DefaultLifecycleProcessor.start Starting beans in phase 2147483647
26-Sep-2017 17:51:22.990 INFO [localhost-startStop-2] org.springframework.web.servlet.DispatcherServlet.initServletBean FrameworkServlet 'dispatcher': initialization completed in 1183 ms

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "C3P0PooledConnectionPoolManager[identityToken->2vylwz9q1glufwn1d1i0o2|260427e]-AdminTaskTimer"

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "I/O dispatcher 1"

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "AsyncFileHandlerWriter-929338653"

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "I/O dispatcher 5"

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "I/O dispatcher 10"

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "Navlink Plugin Executor:thread-2"

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "I/O dispatcher 7"

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "I/O dispatcher 9"

4082,0-1 77%
Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "I/O dispatcher 9"

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "I/O dispatcher 4"
Exception in thread "Navlink Plugin Executor:thread-1" Exception in thread "httpclient-io:thread-1" java.lang.OutOfMemoryError: Java heap space
Exception in thread "ThreadPoolAsyncTaskExecutor::Thread 14" Exception in thread "I/O dispatcher 3" Exception in thread "I/O dispatcher 8" Exception in thread "I/O dispatcher 2" Exception in thread "Navlink Plugin Executor:thread-3" Exception in thread "I/O dispatcher 6" java.lang.OutOfMemoryError: Java heap space
java.lang.OutOfMemoryError: Java heap space
java.lang.OutOfMemoryError: Java heap space
java.lang.OutOfMemoryError: Java heap space
java.lang.OutOfMemoryError: Java heap space
java.lang.OutOfMemoryError: Java heap space
java.lang.OutOfMemoryError: Java heap space

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "Connection evictor"

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "pool-1-thread-1-Logging Task Scheduler"
Exception in thread "C3P0PooledConnectionPoolManager[identityToken->2vylwz9q1glufwn1d1i0o2|3891a099]-AdminTaskTimer" java.lang.OutOfMemoryError: Java heap space
26-Sep-2017 17:56:27.121 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8090"]
26-Sep-2017 17:56:27.137 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 320889 ms

8、http://IP:8090 

The page show :

logo system error.

logoSystem Error

A system error has occurred — our apologies!

For immediate troubleshooting, consult our knowledge base for a solution.

If you would like to receive support from Atlassian's support team, ask your Confluence administrator to create a support issue on Atlassian's support system with the following information:

  1. a description of your problem and what you were doing at the time it occurred
  2. a copy of the error and system information found below
  3. a copy of the application logs (if possible).

Your Confluence administrator can use the support request form to create a support ticket which will include this information.

We will respond as promptly as possible.
Thank you!

Return to site homepage…

Cause

java.lang.reflect.UndeclaredThrowableException
    at com.sun.proxy.$Proxy78.permissionExists(Unknown Source)

caused by: java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

caused by: org.springframework.dao.InvalidDataAccessResourceUsageException: could not extract ResultSet; SQL [n/a]; nested exception is org.hibernate.exception.SQLGrammarException: could not extract ResultSet
    at org.springframework.orm.hibernate5.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:224)

caused by: org.hibernate.exception.SQLGrammarException: could not extract ResultSet
    at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:63)

caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'spacepermi0_.PERMALLUSERSSUBJECT' in 'field list'
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

Stack Trace:[hide]

java.lang.reflect.UndeclaredThrowableException
	at com.sun.proxy.$Proxy78.permissionExists(Unknown Source)
	at com.atlassian.confluence.security.access.DefaultConfluenceAccessManager.hasGlobalPermissionAsUser(DefaultConfluenceAccessManager.java:122)
	at com.atlassian.confluence.security.access.DefaultConfluenceAccessManager.anonymousCanUseConfluence(DefaultConfluenceAccessManager.java:98)
	at com.atlassian.confluence.security.access.DefaultConfluenceAccessManager.getAccessStatusForAnonymous(DefaultConfluenceAccessManager.java:62)
	at com.atlassian.confluence.security.access.DefaultConfluenceAccessManager.getUserAccessStatusNoExemptions(DefaultConfluenceAccessManager.java:54)
	at com.atlassian.confluence.security.access.CachingConfluenceAccessManager.getUserAccessStatusNoExemptions(CachingConfluenceAccessManager.java:38)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
Caused by: java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.atlassian.confluence.impl.security.SpacePermissionManagerFactory.lambda$new$0(SpacePermissionManagerFactory.java:70)
	... 305 more
Caused by: org.springframework.dao.InvalidDataAccessResourceUsageException: could not extract ResultSet; SQL [n/a]; nested exception is org.hibernate.exception.SQLGrammarException: could not extract ResultSet
	at org.springframework.orm.hibernate5.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:224)
	at org.springframework.orm.hibernate5.HibernateTemplate.doExecute(HibernateTemplate.java:366)
	at org.springframework.orm.hibernate5.HibernateTemplate.execute(HibernateTemplate.java:313)
	at com.atlassian.confluence.security.persistence.dao.hibernate.HibernateSpacePermissionDao.executeSpacePermissionQueryBySubject(HibernateSpacePermissionDao.java:135)
	at com.atlassian.confluence.security.persistence.dao.hibernate.HibernateSpacePermissionDao.hasPermission(HibernateSpacePermissionDao.java:37)
	at com.atlassian.confluence.security.CachingSpacePermissionManager.findCachedPermissionOrFetchFromDao(CachingSpacePermissionManager.java:178)
	at com.atlassian.confluence.security.CachingSpacePermissionManager.permissionExists(CachingSpacePermissionManager.java:117)
	... 310 more
Caused by: org.hibernate.exception.SQLGrammarException: could not extract ResultSet
	at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:63)
	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.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:97)
	at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:80)
	at org.hibernate.loader.Loader.getResultSet(Loader.java:2123)
	at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1911)
	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 com.atlassian.confluence.security.persistence.dao.hibernate.HibernateSpacePermissionDao.lambda$executeSpacePermissionQueryBySubject$3(HibernateSpacePermissionDao.java:153)
	at org.springframework.orm.hibernate5.HibernateTemplate.doExecute(HibernateTemplate.java:359)
	... 315 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'spacepermi0_.PERMALLUSERSSUBJECT' in 'field list'
	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:411)
	at com.mysql.jdbc.Util.getInstance(Util.java:386)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1054)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4187)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4119)
	at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2570)
	at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2731)
	at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2815)
	at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2155)
	at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2322)
	at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:379)
	at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:71)
	... 332 more

        9、free -g
        show :
      total used free shared buffers cached
Mem: 15 1 13 0 0 0
-/+ buffers/cache: 1 14
Swap: 3 0 3
11、I need you help.Thank you very much!


 

 

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2 answers

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Steve Shaw
Steve Shaw
Atlassian Team
Atlassian Team members are employees working across the company in a wide variety of roles.
June 26, 2019

While it certainly appears that it would be good to configure Confluence with more memory while performing the upgrade, I'd also recommend that you perform an intermediate upgrade first to version 5.10.x before upgrading to version 6.x based on the "spacepermi0_.PERMALLUSERSSUBJECT" missing column error. 

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Nic Brough -Adaptavist-
Nic Brough -Adaptavist-
Community Leader
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September 26, 2017

You are defining -Xmx twice in setenv.sh and I don't know which one it will be using.  The error message is that it is running out of memory while processing, so I suspect it's using the lower one.  Problem is that it could be a bug (specifically one where it can't handle some of your data) causing it to run out of memory, and later it also looks like you may have a database problem.

My instinct is to try it again, ensuring you are using the higher memory setting, but I can't be sure that will fix it.

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Support_Valiantys
Support_Valiantys
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August 8, 2018

Hi,

Do you find something on this topic?

I have a similar case during an upgrade.

 

Regards

Arnold G

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