Upgrade from old Confluence 3.4.6

Hi support,

I'm upgrading an old Confluence 3.4.6 to the current one. The first step, if I understand, it's to upgrade in the version 3.5.17. I followed the instructions in https://confluence.atlassian.com/display/CONF35/Upgrading+Confluence+Standalone+Distribution, without customization part. But I get a error page in browser, no error in log files. I don't know how I can do.

Error description :
Upgrade failed. Please consult the system logs for details. You will need to fix these problems, restore your database and confluence home directory to the pre upgrade state. Then retry the upgrade.

Server configuration : (Migration test server, an exact copy from the production one with VMWare, only server name was changed to acces)

* 3.5.17 standalone
* local postgrest DB
* OpenLDAP authentication

Thanks for your help.

9 answers

0 vote

"No error in log files" - I'm afraid that simply isn't right. Please check ALL of them, especially the one that definitely says "Upgrade failed" in it.

The only time your log files won't have that in them is if you run out of disk space during the upgrade, so cheeck that first.

Hi Nic,

The following log files in <Installation-Directory>/logs :

-rw-r--r-- 1 confluence confluence 49494 Feb 6 16:50 catalina.2014-02-06.log

-rw-r--r-- 1 confluence confluence 61812 Feb 6 16:50 catalina.out

-rw-r--r-- 1 confluence confluence 0 Feb 6 15:21 host-manager.2014-02-06.log

-rw-r--r-- 1 confluence confluence 0 Feb 6 15:21 localhost.2014-02-06.log

-rw-r--r-- 1 confluence confluence 0 Feb 6 15:21 manager.2014-02-06.log

Maybe these aren't the good files ?
Or the problem is before the upgrade process. DB access is maybe not possible. I don't know. Give you the following log lines (in catalina.2014-02-06.log) after the commands startup.sh and shutdown.sh, failed messages are printed when I shutdown the service, but no failed message when I start the service :
=====
Feb 6, 2014 4:07:03 PM org.apache.tomcat.util.digester.SetPropertiesRule begin
WARNING: [SetPropertiesRule]{Server} Setting property 'debug' to '0' did not find a matching property.
Feb 6, 2014 4:07:04 PM org.apache.tomcat.util.digester.SetPropertiesRule begin
WARNING: [SetPropertiesRule]{Server/Service/Engine} Setting property 'debug' to '0' did not find a matching property.
Feb 6, 2014 4:07:04 PM org.apache.tomcat.util.digester.SetPropertiesRule begin
WARNING: [SetPropertiesRule]{Server/Service/Engine/Host} Setting property 'debug' to '0' did not find a matching property.
Feb 6, 2014 4:07:04 PM org.apache.tomcat.util.digester.SetPropertiesRule begin
WARNING: [SetPropertiesRule]{Server/Service/Engine/Host/Context} Setting property 'debug' to '0' did not find a matching property.
Feb 6, 2014 4:07:04 PM org.apache.coyote.http11.Http11Protocol init
INFO: Initializing Coyote HTTP/1.1 on http-8080
Feb 6, 2014 4:07:05 PM org.apache.coyote.http11.Http11Protocol init
INFO: Initializing Coyote HTTP/1.1 on http-8443
Feb 6, 2014 4:07:05 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 2376 ms
Feb 6, 2014 4:07:05 PM org.apache.catalina.core.StandardService start
INFO: Starting service Tomcat-Standalone
Feb 6, 2014 4:07:05 PM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/6.0.32
Feb 6, 2014 4:07:41 PM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
Feb 6, 2014 4:07:41 PM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8443
Feb 6, 2014 4:07:41 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 35986 ms
Feb 6, 2014 4:15:56 PM org.apache.coyote.http11.Http11Protocol pause
INFO: Pausing Coyote HTTP/1.1 on http-8080
Feb 6, 2014 4:15:56 PM org.apache.coyote.http11.Http11Protocol pause
INFO: Pausing Coyote HTTP/1.1 on http-8443
Feb 6, 2014 4:15:57 PM org.apache.catalina.core.StandardService stop
INFO: Stopping service Tomcat-Standalone
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [] registered the JDBC driver [org.hsqldb.jdbc.JDBCDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [] registered the JDBC driver [com.mysql.jdbc.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [com.google.common.base.internal.Finalizer] but has failed to stop it. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-1] but has failed to stop it. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-2] but has failed to stop it. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-3] but has failed to stop it. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-4] but has failed to stop it. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-5] but has failed to stop it. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-6] but has failed to stop it. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-7] but has failed to stop it. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-8] but has failed to stop it. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-9] but has failed to stop it. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-10] but has failed to stop it. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [Resource Destroyer in BasicResourcePool.close()] but has failed to stop it. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [] created a ThreadLocal with key of type [com.atlassian.core.logging.ThreadLocalErrorCollection$2] (value [com.atlassian.core.logging.ThreadLocalErrorCollection$2@6c87ac60]) and a value of type [java.lang.Boolean] (value [false]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@3f460a4a]) and a value of type [org.dom4j.DocumentFactory] (value [org.dom4j.DocumentFactory@f4da0ba]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [] created a ThreadLocal with key of type [org.apache.log4j.helpers.ThreadLocalMap] (value [org.apache.log4j.helpers.ThreadLocalMap@180aa467]) and a value of type [java.util.Hashtable] (value [{}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Feb 6, 2014 4:15:58 PM org.apache.coyote.http11.Http11Protocol destroy
INFO: Stopping Coyote HTTP/1.1 on http-8080
Feb 6, 2014 4:15:58 PM org.apache.coyote.http11.Http11Protocol destroy
INFO: Stopping Coyote HTTP/1.1 on http-8443
=====
Thanks for your help.
Joe Wai Tye Atlassian Team Feb 06, 2014

Hi,

Could you perhaps check the catalina.out log file for errors? Also, what does the error message say?

Hi Joe,

Log lines are similare.

catalina.out

=====

Feb 6, 2014 4:07:03 PM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server} Setting property 'debug' to '0' did not find a matching property.

Feb 6, 2014 4:07:04 PM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server/Service/Engine} Setting property 'debug' to '0' did not find a matching property.

Feb 6, 2014 4:07:04 PM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server/Service/Engine/Host} Setting property 'debug' to '0' did not find a matching property.

Feb 6, 2014 4:07:04 PM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server/Service/Engine/Host/Context} Setting property 'debug' to '0' did not find a matching property.

Feb 6, 2014 4:07:04 PM org.apache.coyote.http11.Http11Protocol init

INFO: Initializing Coyote HTTP/1.1 on http-8080

Feb 6, 2014 4:07:05 PM org.apache.coyote.http11.Http11Protocol init

INFO: Initializing Coyote HTTP/1.1 on http-8443

Feb 6, 2014 4:07:05 PM org.apache.catalina.startup.Catalina load

INFO: Initialization processed in 2376 ms

Feb 6, 2014 4:07:05 PM org.apache.catalina.core.StandardService start

INFO: Starting service Tomcat-Standalone

Feb 6, 2014 4:07:05 PM org.apache.catalina.core.StandardEngine start

INFO: Starting Servlet Engine: Apache Tomcat/6.0.32

2014-02-06 16:07:12,305 INFO [main] [com.atlassian.confluence.lifecycle] contextInitialized Starting Confluence 3.5.17 (build #2176)

2014-02-06 16:07:15,581 INFO [main] [atlassian.plugin.manager.DefaultPluginManager] init Initialising the plugin system

2014-02-06 16:07:15,961 INFO [main] [atlassian.plugin.manager.DefaultPluginManager] init Plugin system started in 0:00:00.377

Feb 6, 2014 4:07:41 PM org.apache.coyote.http11.Http11Protocol start

INFO: Starting Coyote HTTP/1.1 on http-8080

Feb 6, 2014 4:07:41 PM org.apache.coyote.http11.Http11Protocol start

INFO: Starting Coyote HTTP/1.1 on http-8443

Feb 6, 2014 4:07:41 PM org.apache.catalina.startup.Catalina start

INFO: Server startup in 35986 ms

Feb 6, 2014 4:15:56 PM org.apache.coyote.http11.Http11Protocol pause

INFO: Pausing Coyote HTTP/1.1 on http-8080

Feb 6, 2014 4:15:56 PM org.apache.coyote.http11.Http11Protocol pause

INFO: Pausing Coyote HTTP/1.1 on http-8443

Feb 6, 2014 4:15:57 PM org.apache.catalina.core.StandardService stop

INFO: Stopping service Tomcat-Standalone

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc

SEVERE: The web application [] registered the JDBC driver [org.hsqldb.jdbc.JDBCDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc

SEVERE: The web application [] registered the JDBC driver [com.mysql.jdbc.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc

SEVERE: The web application [] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [com.google.common.base.internal.Finalizer] but has failed to stop it. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-1] but has failed to stop it. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-2] but has failed to stop it. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-3] but has failed to stop it. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-4] but has failed to stop it. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-5] but has failed to stop it. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-6] but has failed to stop it. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-7] but has failed to stop it. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-8] but has failed to stop it. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-9] but has failed to stop it. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-10] but has failed to stop it. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [Resource Destroyer in BasicResourcePool.close()] but has failed to stop it. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap

SEVERE: The web application [] created a ThreadLocal with key of type [com.atlassian.core.logging.ThreadLocalErrorCollection$2] (value [com.atlassian.core.logging.ThreadLocalErrorCollection$2@6c87ac60]) and a value of type [java.lang.Boolean] (value [false]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap

SEVERE: The web application [] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@3f460a4a]) and a value of type [org.dom4j.DocumentFactory] (value [org.dom4j.DocumentFactory@f4da0ba]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.

Feb 6, 2014 4:15:57 PM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap

SEVERE: The web application [] created a ThreadLocal with key of type [org.apache.log4j.helpers.ThreadLocalMap] (value [org.apache.log4j.helpers.ThreadLocalMap@180aa467]) and a value of type [java.util.Hashtable] (value [{}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.

log4j:ERROR LogMananger.repositorySelector was null likely due to error in class reloading, using NOPLoggerRepository.

Feb 6, 2014 4:15:58 PM org.apache.coyote.http11.Http11Protocol destroy

INFO: Stopping Coyote HTTP/1.1 on http-8080

Feb 6, 2014 4:15:58 PM org.apache.coyote.http11.Http11Protocol destroy

INFO: Stopping Coyote HTTP/1.1 on http-8443

=====

The errors you see on this shut-down are almost certainly triggered by the errors as the system starts up, and although they look scary, they don't help much because the problem is happening before them (in fact, you can get these errors from shutting down an apparently healthy Confluence, so they could be a complete red herring)

There will be warnings and errors on startup and those are what we need to see.

Could you start clean - stop confluence, move all the logs out of the directory so that you have an absolutely clean run. Start confluence, give it a couple of minutes, try to hit it with a single browser hit, and then look at the logs. The catalina.out may still be short, but it will show us something.

All the catalina.out with a single startup and shutdown operation started with a empty log file.

I think there is no difference since my last post.

=====

Feb 7, 2014 10:35:55 AM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server} Setting property 'debug' to '0' did not find a matching property.

Feb 7, 2014 10:35:55 AM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server/Service/Engine} Setting property 'debug' to '0' did not find a matching property.

Feb 7, 2014 10:35:55 AM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server/Service/Engine/Host} Setting property 'debug' to '0' did not find a matching property.

Feb 7, 2014 10:35:55 AM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server/Service/Engine/Host/Context} Setting property 'debug' to '0' did not find a matching property.

Feb 7, 2014 10:35:55 AM org.apache.coyote.http11.Http11Protocol init

INFO: Initializing Coyote HTTP/1.1 on http-8080

Feb 7, 2014 10:35:55 AM org.apache.coyote.http11.Http11Protocol init

INFO: Initializing Coyote HTTP/1.1 on http-8443

Feb 7, 2014 10:35:55 AM org.apache.catalina.startup.Catalina load

INFO: Initialization processed in 825 ms

Feb 7, 2014 10:35:55 AM org.apache.catalina.core.StandardService start

INFO: Starting service Tomcat-Standalone

Feb 7, 2014 10:35:55 AM org.apache.catalina.core.StandardEngine start

INFO: Starting Servlet Engine: Apache Tomcat/6.0.32

2014-02-07 10:35:59,824 INFO [main] [com.atlassian.confluence.lifecycle] contextInitialized Starting Confluence 3.5.17 (build #2176)

2014-02-07 10:36:02,500 INFO [main] [atlassian.plugin.manager.DefaultPluginManager] init Initialising the plugin system

2014-02-07 10:36:02,677 INFO [main] [atlassian.plugin.manager.DefaultPluginManager] init Plugin system started in 0:00:00.175

Feb 7, 2014 10:36:22 AM org.apache.coyote.http11.Http11Protocol start

INFO: Starting Coyote HTTP/1.1 on http-8080

Feb 7, 2014 10:36:22 AM org.apache.coyote.http11.Http11Protocol start

INFO: Starting Coyote HTTP/1.1 on http-8443

Feb 7, 2014 10:36:22 AM org.apache.catalina.startup.Catalina start

INFO: Server startup in 26935 ms

Feb 7, 2014 10:48:47 AM org.apache.coyote.http11.Http11Protocol pause

INFO: Pausing Coyote HTTP/1.1 on http-8080

Feb 7, 2014 10:48:47 AM org.apache.coyote.http11.Http11Protocol pause

INFO: Pausing Coyote HTTP/1.1 on http-8443

Feb 7, 2014 10:48:48 AM org.apache.catalina.core.StandardService stop

INFO: Stopping service Tomcat-Standalone

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc

SEVERE: The web application [] registered the JDBC driver [org.hsqldb.jdbc.JDBCDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc

SEVERE: The web application [] registered the JDBC driver [com.mysql.jdbc.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc

SEVERE: The web application [] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [com.google.common.base.internal.Finalizer] but has failed to stop it. This is very likely to create a memory leak.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-1] but has failed to stop it. This is very likely to create a memory leak.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-2] but has failed to stop it. This is very likely to create a memory leak.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-3] but has failed to stop it. This is very likely to create a memory leak.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-4] but has failed to stop it. This is very likely to create a memory leak.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-5] but has failed to stop it. This is very likely to create a memory leak.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-6] but has failed to stop it. This is very likely to create a memory leak.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-7] but has failed to stop it. This is very likely to create a memory leak.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-8] but has failed to stop it. This is very likely to create a memory leak.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-9] but has failed to stop it. This is very likely to create a memory leak.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [] appears to have started a thread named [QuartzScheduler_Worker-10] but has failed to stop it. This is very likely to create a memory leak.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap

SEVERE: The web application [] created a ThreadLocal with key of type [com.atlassian.core.logging.ThreadLocalErrorCollection$2] (value [com.atlassian.core.logging.ThreadLocalErrorCollection$2@31109962]) and a value of type [java.lang.Boolean] (value [false]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.

Feb 7, 2014 10:48:49 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap

SEVERE: The web application [] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@38c60a18]) and a value of type [org.dom4j.DocumentFactory] (value [org.dom4j.DocumentFactory@51c0cac6]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.

log4j:ERROR LogMananger.repositorySelector was null likely due to error in class reloading, using NOPLoggerRepository.

Feb 7, 2014 10:48:50 AM org.apache.coyote.http11.Http11Protocol destroy

INFO: Stopping Coyote HTTP/1.1 on http-8080

Feb 7, 2014 10:48:50 AM org.apache.coyote.http11.Http11Protocol destroy

INFO: Stopping Coyote HTTP/1.1 on http-8443

=====

Ok, and that is *just* the log from startup? You have not run the shutdown as well? I'm just trying to establish if you are kicking off the shutdown, or if Tomcat is doing it automatically for you.

The startup wasn't long, it spended maybe 45 seconds, I checked the activities with htop. I shut it down manually.

Right, so you've copied us a huge chunk of log we explicitly didn't want. Ok, we can ignore it, at least we know.

Could you do this again, but instead of stopping it, hit it with a browser. Then get the log (without all the shutdown stuff) and what the browser does (even if it is just a blank screen and a timeout)

The page on the browser wasn't blank, I posted the error description on my first message ready.

Error description :
Upgrade failed. Please consult the system logs for details. You will need to fix these problems, restore your database and confluence home directory to the pre upgrade state. Then retry the upgrade.

catalina.out without shutdown
=====

Feb 10, 2014 2:11:40 PM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server} Setting property 'debug' to '0' did not find a matching property.

Feb 10, 2014 2:11:40 PM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server/Service/Engine} Setting property 'debug' to '0' did not find a matching property.

Feb 10, 2014 2:11:40 PM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server/Service/Engine/Host} Setting property 'debug' to '0' did not find a matching property.

Feb 10, 2014 2:11:40 PM org.apache.tomcat.util.digester.SetPropertiesRule begin

WARNING: [SetPropertiesRule]{Server/Service/Engine/Host/Context} Setting property 'debug' to '0' did not find a matching property.

Feb 10, 2014 2:11:40 PM org.apache.coyote.http11.Http11Protocol init

INFO: Initializing Coyote HTTP/1.1 on http-8080

Feb 10, 2014 2:11:41 PM org.apache.coyote.http11.Http11Protocol init

INFO: Initializing Coyote HTTP/1.1 on http-8443

Feb 10, 2014 2:11:41 PM org.apache.catalina.startup.Catalina load

INFO: Initialization processed in 833 ms

Feb 10, 2014 2:11:41 PM org.apache.catalina.core.StandardService start

INFO: Starting service Tomcat-Standalone

Feb 10, 2014 2:11:41 PM org.apache.catalina.core.StandardEngine start

INFO: Starting Servlet Engine: Apache Tomcat/6.0.32

2014-02-10 14:11:45,032 INFO [main] [com.atlassian.confluence.lifecycle] contextInitialized Starting Confluence 3.5.17 (build #2176)

2014-02-10 14:11:47,570 INFO [main] [atlassian.plugin.manager.DefaultPluginManager] init Initialising the plugin system

2014-02-10 14:11:47,739 INFO [main] [atlassian.plugin.manager.DefaultPluginManager] init Plugin system started in 0:00:00.167

Feb 10, 2014 2:12:08 PM org.apache.coyote.http11.Http11Protocol start

INFO: Starting Coyote HTTP/1.1 on http-8080

Feb 10, 2014 2:12:08 PM org.apache.coyote.http11.Http11Protocol start

INFO: Starting Coyote HTTP/1.1 on http-8443

Feb 10, 2014 2:12:08 PM org.apache.catalina.startup.Catalina start

INFO: Server startup in 26690 ms

=====

Thanks for your efforts

Can you post your atlassian-confluence.log?

Hi Steve,

(atlassian-confluence.log)

Thanks for your help.

I'm rather confused as to why you said "there were no errors in the log" and now you've managed to post thousands of lines of errors.

Anyway, those are showing that your LDAP connection is broken, your classpath is including broken stuff or you're on an incompatible java (possibly both), or that your "upgrade" was done by "unpack new confluence and copy it over the top of the old one, ignoring the fact different libraries are present and may not be deleted".

I'd be tempted to step back from the attempt to upgrade at first. Install a new, clean, empty copy of Confluence and get that working against an empty database.

Hi Nic,

Thanks for your reply.

I know you help us and you have a lot of questions in the ticketing system. But please read entire message content. In my second message, I said : "Maybe these aren't the good files ?". I'm not a specialist of Confluence and I didn't know there is atlassian-confluence.log in other repertory. Steven was the first that mentions this log file in this topic. For other reply, it asked only catalina.out. You're an expert, I trust you to guide me.

Ok, I will follow your instruction. I unpack the new one over the old one.

I'm really surprise that the online upgrade documentation doesn't work. I understand right now why the previous engineer didn't upgrade it.

Thanks for your help.

Don't unpack the new confluence over your old confluence. Nic assumes that have doine this allready.

First, get your old instance working again with a backup

Second, setup a new instance of confluence again a new database

Third, copy your database and do the migration with the new database

And then, pray ;)

One more point, we need clean logs. Please try to clean your logs before starting confluence, as I can see from the log you attached, that there is something missing. Maybe you have to increase the allowed logfilesize.

Thanks Steve.

All the way, I'm on a upgrade test instance. There is no impact in the prod. About my upgrade test, I didn't unpack the new one on the old one.

About the 3rd step, copy the DB and do the migration. You mean copy all old DB structure with data in a new DB instance. And than "do the migration", but how to migrate ??? Just startup Confluence ?

Ok, I will have a look about the logfilesize.

Thanks

From my experience I expect, that your database is now broken and will not work with the old version of confluence. That's why you need a backup.

If your old confluence version is working with the backup, then setup the new confluence-version using a copy of your home directory and a copy of the database, you can change the dburl in your confluence.cfg.xml in the confluence_home directory.

This will provide you a save and fast rollback option on your production later ;)

So before starting to process above, I started Confluence with the existed version 3.4.6 (same one at the right now prod version) without DB backup restauration (it means I use the existed DB). Confluence is running. I can authenticate with my account and update content.

I will fellow your instructions later in the afternoon, I just have other emmergencies.

Thanks for your help.
:)

Hi,

Sorry for this later reply. I had other emergency.
So, I :

  1. made a new DB with the prod one (useful one with old version)
  2. change the same DB owner as the previous one
  3. configured the new DB name in confluence.cfg.xml
  4. startup.sh and waiting a few minutes
  5. browser the frontpage

--> The same error.

Have you started with a completely clean system again?

It's depend what do you define "completely clean system". Is there an indication in administration interface ?

I used a copy with the prod one which is working fine.

Thanks for your help.

Your original posting strongly implied that you'd installed a new confluence over an old one, hooked it up to the old database and probably damaged the database.

A clean system is one that you have installed in a clean, empty space, and restored an undamaged database into it before starting it.

Is that what you have done?

I've never installed a new confluence over the old one. Please read messages. I misunderstood that you talk me to install the new one over the old in the message Feb 10 at 04:32 PM. Hope that Steve gave me the correct instructions.

I reply again, the last installation was used a copy of the prod instance. Prod instance works fine.

I wrote all operations that I did. Don't you read ?

Yes, I read, but you're expecting us to go over everything you've posted piecemeal, and frankly, it really isn't clear what you've been doing. At no point do you say you've unpacked a clean copy, if you would care to re-read the 12 pages of conversation.

This current answer/comment thread starts with you saying you've done the basics of an installation, and then says "same error" without saying WHICH "same error" it is.

It really is not clear what you are doing here. So, for clarity, could you tell us what you have done from scratch. Exact details aren't too important, it's the starting point.

So, could you

1. Confirm what I am hoping you have done: Installed confluence into an empty directory, told it to use a new empty data directory, configured it to use an empty database, and started it. Followed the standard installation instructions, and hence expected to get a "welcome to your new confluence" page. (OR, tell us where you've diverged from that)

2. Tell us what the error is.

Ok Nic, you're the King, you're the God. No problem.

I feel that I turn around, I'll live with. From the beginning, I did the upgrade as you said in your point 1. I followed the instructions in https://confluence.atlassian.com/display/CONF35/Upgrading+Confluence+Standalone+Distribution. In section Performing the Upgrade point 4. "Use your unzip program to unzip the installation file. You should now have a new directory called confluence-<version>", that was I did.

So I will do it AGAIN for your pleasure.

Thanks for your help.

<sigh> It's not what you're doing (probably), just the lack of clarity, not answering the questions we've asked you, and not really reading what we're asking.

Even in this comment, you've said "I did the upgrade as you said in point 1", but not said which point 1. The point 1 from my last comment was NOT an upgrade, the whole point of it is to make sure you can create an empty, fresh, clean confluence.

Then you say you've followed the instructions in the docs and got a new directory with a new confluence in it, which might work, but there's not much detail.

In both cases, you've not given us the errors...

Thank you for the criticism God, it helps me a lot in advance. Please God, don't said "probably", because you are the God and you are the truth.

Please God let me time to redo again the same installation and get it back maybe "new" errors.

Your pleasure is mine.

0 vote

Hi there,


Looking at your logs, it seem like the issue is related to some missing constraint problem in your Confluence table. I suggest you to run the following query. *Remember to backup your Confluence database before running the queries below.

alter table bandana drop constraint bandana_unique_key;
alter table CONTENT_PERM drop constraint cp_unique_user;
alter table CONTENT_PERM drop constraint cp_unique_group;
alter table CONTENT_PERM_SET drop constraint cps_unique_type;
delete from CONTENT_PERM where CPS_ID is null;
delete from CONTENT_PERM_SET where CONTENT_ID is null;

An important note! These SQL commands solve the problem also when importing data that has been exported from Jira 3.4.6, but only if you execute them after the import process has started. If you run them before, they will have no effect because at the beginning of the import bandana_unique_key constraint is recreated.

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