Migrating and upgrading Jira 4.2 to latest

Hi,

I need to migrate Jira 4.2 Enterprise version to a new server. I also want to upgrade to latest jira version. What i have done is, in short (from the guide upgrade manually):

Server A = Old server with jira 4.2

Server B = New server which is empty but will eventually have latest jira

1. On B, followed the guide Installing Jira WAR (latest version) https://confluence.atlassian.com/display/JIRA/Installing+JIRA+WAR

2. On A, copied the jira home /use/local/jira to B

2. On A, copied the database to B and restored it to mysql

This did work out first, but after a restart nothing works anymore. So i removed everything and followed the above steps a second time, and now i get this error:

The following plugins are required by JIRA, but have not been started: Embedded Gadgets Plugin (com.atlassian.gadgets.embedded), Gadget Dashboard Plugin (com.atlassian.gadgets.dashboard), Gadget Directory Plugin (com.atlassian.gadgets.directory), Atlassian JIRA - Plugins - Gadgets Plugin (com.atlassian.jira.gadgets)

I guess i have missed something, so my first question is if the above steps are the correct ones for migrate and upgrade? Any ideas regarding the errors above?
Any help appreciated.

4 answers

Hi, can you please describe your setup? What version of Java and Tomcat have you deployed your WAR to? Also is this on a VM or physical server? How much memory have you allocated?

Hi, memory might be the issue. Later versions of JIRA do use more memory, especially if you've got plugins like greenhopper. The upgrade process itself also consumes more memory as you need a full re-index.

Also I'd advice using Tomcat 6.0.32 as per https://confluence.atlassian.com/display/JIRA/Supported+Platforms.

Ok here is some more info:

Server A (VM):

java = 1.6.0.24

mysql = 5.0

tomcat = 6.0.29

Server B (VM):

java = 1.6.0.24

mysql = 5.5

tomcat = 6.0.35

And this is from setenv.sh on both A and B:

export CATALINA_OPTS="$CATALINA_OPTS -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true -Xms128m -Xmx512m -XX:MaxPermSize=256m"

Thank you. I will try to increase the memory but wouldn't the logs specifically report memory problems? I also read on some other threads that you cant just copy the jira home directory to new server including all plugins because some plugins are not compatible with new jira version. So how can i solve that? I can only see one plugin in /usr/local/jira/plugins/installed-plugins folder so where are the others?

No, it is not smart enough to report memory problems :). It is best to check the plugin requirements first before an upgrade. However, if the plugins themselves do have errors on startup this should show in the logs.

There is still alot of errors after a third retry. This time i installed the preferred tomcat version 6.0.32, i also increased the memory and removed .bundled_plugins and .osgi-plugins.

From the catalina.out:

2012-09-06 14:04:10,088 main WARN [core.entity.jdbc.DatabaseUtil] Field "disabled" of entity "CustomFieldOption" is missing its corresponding column "disabled"

And so it contiunes. Then the plugin errors:
2012-09-06 14:09:26,226 main INFO [atlassian.plugin.loaders.ScanningPluginLoader] Plugin Unit: /usr/local/jira/plugins/.bundled-plugins/workflow-designe
r-plugin-2.6.13.jar (1344964058000) created
2012-09-06 14:11:36,312 Timer-1 WARN [internal.dependencies.startup.DependencyWaiterApplicationContextExecutor] Timeout occurred before finding service
dependencies for [NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.administration.atlassian-admin-quicksearch-jira, config=osgibundle:/META-
INF/spring/*.xml)]
2012-09-06 14:11:37,731 Timer-1 ERROR [internal.dependencies.startup.DependencyWaiterApplicationContextExecutor] Unable to create application context for [com.atlassian.administration.atlassian-admin-quicksearch-jira], unsatisfied dependencies...
at java.util.TimerThread.mainLoop(Timer.java:512)
at java.util.TimerThread.run(Timer.java:462)
2012-09-06 14:11:38,469 Timer-1 WARN [internal.dependencies.startup.DependencyWaiterApplicationContextExecutor] Timeout occurred before finding service
dependencies for [NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.applinks.plugin, config=osgibundle:/META-INF/spring/*.xml)]
Final errors show:

The following plugins are required by JIRA, but have not been started:

  • Atlassian JIRA - Plugins - Project Config Plugin (com.atlassian.jira.jira-project-config-plugin)
  • Atlassian OAuth Admin Plugin (com.atlassian.oauth.admin)
  • ... and some more plugins
Any ideas?

One other thing, when i try to shutdown jira via tomcat shutdown.sh i get some errors:

Sep 6, 2012 2:42:40 PM org.apache.catalina.connector.Connector pause

SEVERE: Protocol handler pause failed

java.net.ConnectException: Connection timed out

2012-09-06 14:44:28,123 main ERROR [internal.util.concurrent.RunnableTimedExecution] Closing runnable for context NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.jira.mail-plugin, config=osgibundle:/META-INF/spring/*.xml) did not finish in 10000ms; consider taking a snapshot and then shutdown the VM in case the thread still hangs
Exception in thread "Thread-37" java.lang.NullPointerException
2012-09-06 14:46:03,886 jira-monitoring-plugin ERROR [jira.plugins.monitor.MetricsCollectorTask] Error running task
java.lang.IllegalStateException: RRD already closed, cannot store this sample
Sep 6, 2012 2:47:57 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/jira] appears to have started a thread named [Abandoned connection cleanup thread] but has failed to stop it. This is very likely to create a memory leak.
... and so on.
Only solution is to kill -9 the java process.

There is still alot of errors after a third retry. This time i installed the preferred tomcat version 6.0.32, i also increased the memory and removed .bundled_plugins and .osgi-plugins.

From the catalina.out:

2012-09-06 14:04:10,088 main WARN [core.entity.jdbc.DatabaseUtil] Field "disabled" of entity "CustomFieldOption" is missing its corresponding column "disabled"

And so it contiunes. Then the plugin errors:
2012-09-06 14:09:26,226 main INFO [atlassian.plugin.loaders.ScanningPluginLoader] Plugin Unit: /usr/local/jira/plugins/.bundled-plugins/workflow-designe
r-plugin-2.6.13.jar (1344964058000) created
2012-09-06 14:11:36,312 Timer-1 WARN [internal.dependencies.startup.DependencyWaiterApplicationContextExecutor] Timeout occurred before finding service
dependencies for [NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.administration.atlassian-admin-quicksearch-jira, config=osgibundle:/META-
INF/spring/*.xml)]
2012-09-06 14:11:37,731 Timer-1 ERROR [internal.dependencies.startup.DependencyWaiterApplicationContextExecutor] Unable to create application context for [com.atlassian.administration.atlassian-admin-quicksearch-jira], unsatisfied dependencies...
at java.util.TimerThread.mainLoop(Timer.java:512)
at java.util.TimerThread.run(Timer.java:462)
2012-09-06 14:11:38,469 Timer-1 WARN [internal.dependencies.startup.DependencyWaiterApplicationContextExecutor] Timeout occurred before finding service
dependencies for [NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.applinks.plugin, config=osgibundle:/META-INF/spring/*.xml)]
Final errors show:

The following plugins are required by JIRA, but have not been started:

  • Atlassian JIRA - Plugins - Project Config Plugin (com.atlassian.jira.jira-project-config-plugin)
  • Atlassian OAuth Admin Plugin (com.atlassian.oauth.admin)
  • ... and some more plugins
Any ideas?

I see you are using Mysql 5.0 which is not supported, isn't that a problem?

This is mostly due to the lack of CPU resources for the VM, how many VMs are there in the host? And what is the CPU reservation for this VM? And what else is running in that VM?

Please check the minimum recommendations for running JIRA at https://confluence.atlassian.com/display/JIRA/JIRA+Requirements#JIRARequirements-JIRAServerHardwareRecommendations

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