JIRA won't reindex.

[Kristen Viscardi]

Our JIRA keeps getting stuck at 6% when we re-index. We have increased the time out time and nothing is working. 

[Alok Singh]

you need to cleanup your jira cache in the home directory JIRA_HOME/caches/ and then restart jira. If that does not work then you may have to shutdown jira and then do some clean in the folders like JIRA_HOME\plugins\.osgi-plugins and JIRA_HOME\plugins\.bundled-plugins

[Nic Brough -Adaptavist-]

Ah-ha!  You have a broken add-on.

1. check the version of the "Root Cause Analysis" add-on - is it definitely the latest version available for your version of JIRA (If you're not sure of that and need our help, you'll need to tell us what version of the add-on you have and what version of JIRA.  The full exact versions from the "system information" page).
   1. If it's a dodgy version, upgrade it, or move to a valid one, and re-index
   2. If it's a valid combination, then continue as below:
2. Disable the add-on and re-index
3. If still broken, remove the add-on and re-index

If 2 or 3 fixes the problem, then you'll need to report this one to the vendor of the add-on, as there's a bug in their code.

[Deleted user]

What does the log say?

[Kristen Viscardi]

The log says the issues are timing out.

[Nic Brough -Adaptavist-]

We need more than that, we already know it's timing out.

[Kristen Viscardi]

2015-12-22 17:36:15,105 IssueIndexer:thread-9 ERROR VonUser 1048x431x6 yfhsr9 10.111.103.226 /secure/admin/IndexReIndex.jspa [jira.issue.index.Defa ultIndexManager] Could not reindex: com.atlassian.jira.issue.util.IssueObjectIssuesIterable (1 items): [QACR-2520] 2015-12-22 17:36:15,240 IssueIndexer:thread-6 ERROR VonUser 1048x431x6 yfhsr9 10.111.103.226 /secure/admin/IndexReIndex.jspa [jira.issue.index.Defa ultIndexManager] Wait attempt timed out - waited 150000 milliseconds com.atlassian.jira.issue.index.IndexException: Wait attempt timed out - waited 150000 milliseconds at com.atlassian.jira.issue.index.DefaultIndexManager.obtain(DefaultIndexManager.java:936) at com.atlassian.jira.issue.index.DefaultIndexManager.access$900(DefaultIndexManager.java:97) at com.atlassian.jira.issue.index.DefaultIndexManager$IndexLock.tryLock(DefaultIndexManager.java:1298) at com.atlassian.jira.issue.index.DefaultIndexManager.getIndexLock(DefaultIndexManager.java:917) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:594) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssueObjects(DefaultIndexManager.java:473) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndex(DefaultIndexManager.java:497) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndex(DefaultIndexManager.java:479) at sun.reflect.GeneratedMethodAccessor760.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83) at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28) at com.sun.proxy.$Proxy15.reIndex(Unknown Source) at com.avant.plugins.jira.rootcauseanalysis.RootCauseAnalysisPluginCommonUtilities.reindex(RootCauseAnalysisPluginCommonUtilities.java:234) at com.avant.plugins.jira.rootcauseanalysis.ao.RootCauseAnalysisItemServiceImpl.createRCAItemWithKey(RootCauseAnalysisItemServiceImpl.java: 294) at com.avant.plugins.jira.rootcauseanalysis.ao.RootCauseAnalysisItemServiceImpl.getObjectFromKey(RootCauseAnalysisItemServiceImpl.java:321) at com.avant.plugins.jira.rootcauseanalysis.customfields.RootCauseAnalysisIssueCustomField.getValueFromIssue(RootCauseAnalysisIssueCustomFi eld.java:25) at com.atlassian.jira.issue.fields.CustomFieldImpl.getValue(CustomFieldImpl.java:454) at com.atlassian.jira.issue.index.indexers.impl.ExactTextCustomFieldIndexer.addDocumentFields(ExactTextCustomFieldIndexer.java:39) at com.atlassian.jira.issue.index.indexers.impl.ExactTextCustomFieldIndexer.addDocumentFieldsSearchable(ExactTextCustomFieldIndexer.java:29 ) at com.atlassian.jira.issue.index.indexers.impl.AbstractCustomFieldIndexer.addIndex(AbstractCustomFieldIndexer.java:46) at com.atlassian.jira.issue.index.DefaultIssueDocumentFactory$Builder.add(DefaultIssueDocumentFactory.java:102) at com.atlassian.jira.issue.index.DefaultIssueDocumentFactory$Builder.addAll(DefaultIssueDocumentFactory.java:91) at com.atlassian.jira.issue.index.DefaultIssueDocumentFactory.apply(DefaultIssueDocumentFactory.java:60) at com.atlassian.jira.issue.index.DefaultIssueDocumentFactory.apply(DefaultIssueDocumentFactory.java:37) at com.atlassian.jira.issue.index.DefaultIssueIndexer$DefaultDocumentCreationStrategy.get(DefaultIssueIndexer.java:644) at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:427) at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:412) at com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:334) at com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:330) at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:9) at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:5) at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:38) at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:35) at com.atlassian.jira.util.concurrent.BoundedExecutor$2.call(BoundedExecutor.java:85) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) 2015-12-22 17:36:15,243 IssueIndexer:thread-6 ERROR VonUser 1048x431x6 yfhsr9 10.111.103.226 /secure/admin/IndexReIndex.jspa [jira.issue.index.Defa ultIndexManager] Could not reindex: com.atlassian.jira.issue.util.IssueObjectIssuesIterable (1 items): [QACR-2518]

[Martin Cleaver]

Also, try disabling JIRA Agile before you reindex. It's not a solution but there's a known issue with Agile.

[Kristen Viscardi]

I tried disabling this plugin and it seemed to be working better. Now it's stuck again.

[Martin Cleaver]

Then it's not to do with https://jira.atlassian.com/browse/GHS-12094

[Martin Cleaver]

So I'd bisect the plugins, try to figure out which plugin is the problem.

[Vasiliy Zverev]

Try to do integrity check (admin panel => system => integrity check)