how to confluence update from 5.1.3 to 6.2-6.4

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!


 

 

1 answer

0 vote

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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