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Indexing fails with Reindex All FAILED error

Manu Mishra

Every week we performs a JIRA Background Re-Indexing and most of the time it fails at 97% with the below error.

 2018-06-09 16:57:53,355 ISSUE-indexQueue:thread-1 INFO gec-jirasvc [action.admin.index.IndexAdminImpl] Re-indexing is 93% complete. Current index: Issue
 2018-06-09 17:02:38,574 ISSUE-indexQueue:thread-1 INFO gec-jirasvc [action.admin.index.IndexAdminImpl] Re-indexing is 94% complete. Current index: Issue
 2018-06-09 17:07:17,169 ISSUE-indexQueue:thread-1 INFO gec-jirasvc [action.admin.index.IndexAdminImpl] Re-indexing is 95% complete. Current index: Issue
 2018-06-09 17:11:54,462 ISSUE-indexQueue:thread-1 INFO gec-jirasvc [action.admin.index.IndexAdminImpl] Re-indexing is 96% complete. Current index: Issue
 2018-06-09 17:16:33,357 ISSUE-indexQueue:thread-1 INFO gec-jirasvc [action.admin.index.IndexAdminImpl] Re-indexing is 97% complete. Current index: Issue
xx.xx.xx.xxx,xx.xx.xx.xx 2018-06-09 17:17:41,441 http-bio-8081-exec-12904 WARN anonymous 1037x11155008x2 - /plugins/servlet/streams [auth.trustedapps.filter.TrustedApplicationFilterAuthenticator] User 'vn0l52t' referenced by trusted application: 'jira:8098344' is not found.
xx.xx.xx.xxx,xx.xx.xx.xx 2018-06-09 17:18:42,044 JiraTaskExectionThread-508 INFO abcde 541x10981514x3 116sphq /secure/admin/IndexReIndex.jspa [jira.issue.index.DefaultIndexManager] 1643701 issues reindexed in the background, in 29826927 millis.
xx.xx.xx.xxx,xx.xx.xx.xx 2018-06-09 17:18:43,893 JiraTaskExectionThread-508 ERROR abcde 541x10981514x3 116sphq /secure/admin/IndexReIndex.jspa [jira.util.index.CompositeIndexLifecycleManager] Reindex All In Background FAILED. Indexer: DefaultIndexManager: paths: [/app/jira-home/caches/indexes/comments, /app/jira-home/caches/indexes/issues, /app/jira-home/caches/indexes/changes, /app/jira-home/caches/indexes/worklogs]
java.lang.NullPointerException
 at com.atlassian.jira.issue.index.DefaultIssueIndexer$3.consume(DefaultIssueIndexer.java:337)
 at com.atlassian.jira.issue.index.DefaultIssueIndexer$3.consume(DefaultIssueIndexer.java:321)
 at com.atlassian.jira.util.collect.CollectionUtil.foreach(CollectionUtil.java:44)
 at com.atlassian.jira.issue.util.IssueIdsIssueIterable.foreach(IssueIdsIssueIterable.java:27)
 at com.atlassian.jira.issue.index.DefaultIssueIndexer.perform(DefaultIssueIndexer.java:320)
 at com.atlassian.jira.issue.index.DefaultIssueIndexer.reindexIssues(DefaultIssueIndexer.java:174)
 at com.atlassian.jira.index.IssueIndexHelper.fixupConcurrentlyIndexedIssues(IssueIndexHelper.java:117)
 at com.atlassian.jira.issue.index.DefaultIndexManager.doBackgroundReindex(DefaultIndexManager.java:1095)
 at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:322)
 at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssuesInBackground(DefaultIndexManager.java:414) <+3> (NativeMethodAccessorImpl.java:62) (DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:498)
 at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83)
 at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28)
 at com.sun.proxy.$Proxy15.reIndexIssuesInBackground(Unknown Source)
 at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexIssuesInBackground(CompositeIndexLifecycleManager.java:123)
 at com.atlassian.jira.web.action.admin.index.ReIndexBackgroundIndexerCommand.doReindex(ReIndexBackgroundIndexerCommand.java:37)
 at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:59)
 at com.atlassian.jira.web.action.admin.index.ReIndexBackgroundIndexerCommand.call(ReIndexBackgroundIndexerCommand.java:16)
 at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:24)
 at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:528)
 at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:491)
 at java.util.concurrent.FutureTask.run(FutureTask.java:266)
 at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
 at java.util.concurrent.FutureTask.run(FutureTask.java:266)
 at com.atlassian.jira.task.ForkedThreadExecutor$ForkedRunnableDecorator.run(ForkedThreadExecutor.java:254)
 at java.lang.Thread.run(Thread.java:745)
xx.xx.xx.xxx,xx.xx.xx.xx 2018-06-09 17:18:43,893 JiraTaskExectionThread-508 INFO abcde 541x10981514x3 116sphq /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing finished
xx.xx.xx.xxx,xx.xx.xx.xx 2018-06-09 17:18:43,893 JiraTaskExectionThread-508 ERROR abcde 541x10981514x3 116sphq /secure/admin/IndexReIndex.jspa [atlassian.jira.task.TaskManagerImpl] Task 'JIRA Indexing' failed.
java.lang.NullPointerException
 at com.atlassian.jira.issue.index.DefaultIssueIndexer$3.consume(DefaultIssueIndexer.java:337)
 at com.atlassian.jira.issue.index.DefaultIssueIndexer$3.consume(DefaultIssueIndexer.java:321)
 at com.atlassian.jira.util.collect.CollectionUtil.foreach(CollectionUtil.java:44)
 at com.atlassian.jira.issue.util.IssueIdsIssueIterable.foreach(IssueIdsIssueIterable.java:27)
 at com.atlassian.jira.issue.index.DefaultIssueIndexer.perform(DefaultIssueIndexer.java:320)
 at com.atlassian.jira.issue.index.DefaultIssueIndexer.reindexIssues(DefaultIssueIndexer.java:174)
 at com.atlassian.jira.index.IssueIndexHelper.fixupConcurrentlyIndexedIssues(IssueIndexHelper.java:117)
 at com.atlassian.jira.issue.index.DefaultIndexManager.doBackgroundReindex(DefaultIndexManager.java:1095)
 at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:322)
 at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssuesInBackground(DefaultIndexManager.java:414) <+3> (NativeMethodAccessorImpl.java:62) (DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:498)
 at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83)
 at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28)
 at com.sun.proxy.$Proxy15.reIndexIssuesInBackground(Unknown Source)
 at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexIssuesInBackground(CompositeIndexLifecycleManager.java:123)
 at com.atlassian.jira.web.action.admin.index.ReIndexBackgroundIndexerCommand.doReindex(ReIndexBackgroundIndexerCommand.java:37)
 at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:59)
 at com.atlassian.jira.web.action.admin.index.ReIndexBackgroundIndexerCommand.call(ReIndexBackgroundIndexerCommand.java:16)
 at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:24)
 at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:528)
 at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:491)
 at java.util.concurrent.FutureTask.run(FutureTask.java:266)
 at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
 at java.util.concurrent.FutureTask.run(FutureTask.java:266)
 at com.atlassian.jira.task.ForkedThreadExecutor$ForkedRunnableDecorator.run(ForkedThreadExecutor.java:254)
 at java.lang.Thread.run(Thread.java:745)

Kindly let me know the potential cause.

Accepted answers

All comments

Moses Thomas_08kyb0

@Manu Mishra Try the resolution related to jira-issue, as i can see from the Log, the error abcde with a Null-Pointer Exception, so it could be that there is a null issue num entry in the jiraissue table.

This could fix your problem.

https://confluence.atlassian.com/jirakb/indexing-fails-with-reindex-all-failed-error-429917142.html

Best!

Manu Mishra

@Moses Thomas I have already applied the fix mentioned in KB article. Though I forgot to mention in description. I am still facing the same error.

Danyal Iqbal

backup the database and execute:

DELETE FROM jiraissue WHERE issuenum IS NULL;

in your db.manager.

Manu Mishra

@Danyal Iqbal how to perform delete operation in db.manger. please refer if any defined process is there. Also is this the only cause of Re-Indexing failure?

Nic Brough -Adaptavist-

"db.manager" means "whatever tool it is you would normally use to directly access the database to run SQL queries on it".

I would also seriously question why you are re-indexing every week - that, plus the fact you are getting errors smacks of something very wrong that you should be fixing instead of running regular indexing.

Manu Mishra

@Nic Brough -Adaptavist- we are running Re-Indexing every weekend because we have a very big instance and there are always some modifications happens. To synchronise the data we are required to run Re-Indexing every weekend when there is no load on server.

We are using SQL developer tool to access dB. Will this syntax run on that?

Also is there any pre-built script or service in Script Runner we can utilize to automate our regular weekend Re-Indexing?

Can you please elaborate more on "getting errors smacks of something very wrong that you should be fixing"

Moses Thomas_08kyb0

@Manu Mishra

Diagnosis

SELECT id, issuenum, project FROM  jiraissue WHERE  issuenum is NULL;

Possible Root Cause

NULL value under the issuenum column of jirraissue table
Ticket registered to atlassian as a bug JSWSERVER-16473

Possible solution.

If the query from the diagnosis returns any results, run the following to remove the NULL entries:

DELETE FROM jiraissue WHERE issuenum IS NULL;

Have you tried this one from your data base server ? make sure you backup you Jira database when performing the delete query in-case.

Best

Manu Mishra

@Moses Thomas we always check the integrity before running re-index. However we still gets the error after validating integrity. I not sure what is conflicting.

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