read past EOF error in jira. Also unable to reindex. Am getting more errors

[Kaboya]

Am getting a read Past EOF Exception when loading my issues within Jira. 

On checking online, the docs advised to rebuild index. 

However when I tried to rebuild index it still failed and asks to check logs. 

Cant decipher anything from these logs. Kindly advise. 

All i can see is reindexing failed? What should someone do in that scenario. 

2018-05-11 16:57:05,379 JiraTaskExectionThread-1 INFO admin 1017x106x1 w6vum4 my-ipaddress /secure/admin/IndexReIndex.jspa [c.a.j.w.a.admin.index.IndexAdminImpl] Re-indexing started
2018-05-11 16:57:05,380 JiraTaskExectionThread-1 INFO admin 1017x106x1 w6vum4 my-ipaddress /secure/admin/IndexReIndex.jspa [c.a.j.util.index.CompositeIndexLifecycleManager] Reindex All starting...
2018-05-11 16:57:05,381 JiraTaskExectionThread-1 INFO admin 1017x106x1 w6vum4 my-ipaddress /secure/admin/IndexReIndex.jspa [c.a.j.w.a.admin.index.IndexAdminImpl] Re-indexing is 0% complete. Current index: Issue
2018-05-11 16:57:05,382 JiraTaskExectionThread-1 INFO admin 1017x106x1 w6vum4 my-ipaddress /secure/admin/IndexReIndex.jspa [c.a.j.issue.index.DefaultIndexManager] ReindexAll in foreground: {indexIssues=true, indexChangeHistory=true, indexComments=true, indexWorklogs=true, forceReloadFromDatabase=false}
2018-05-11 16:57:07,403 JiraTaskExectionThread-1 ERROR admin 1017x106x1 w6vum4 my-ipaddress /secure/admin/IndexReIndex.jspa [c.a.j.util.index.CompositeIndexLifecycleManager] Reindex All FAILED. Indexer: DefaultIndexManager: paths: [/var/atlassian/application-data/jira/caches/indexes/comments, /var/atlassian/application-data/jira/caches/indexes/issues, /var/atlassian/application-data/jira/caches/indexes/changes, /var/atlassian/application-data/jira/caches/indexes/worklogs]
com.atlassian.jira.util.RuntimeIOException: java.io.IOException: read past EOF
 at com.atlassian.jira.index.DefaultIndexEngine.clean(DefaultIndexEngine.java:178)
 at com.atlassian.jira.index.DefaultManager.deleteIndexDirectory(DefaultManager.java:45)
 at com.atlassian.jira.issue.index.DefaultIssueIndexer.deleteIndexes(DefaultIssueIndexer.java:228)
 at com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:990)
 at com.atlassian.jira.issue.index.DefaultIndexManager.lambda$reIndexAll$0(DefaultIndexManager.java:328)
 at com.atlassian.jira.issue.index.DefaultIndexManager.withReindexLock(DefaultIndexManager.java:377)
 at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:328)
 at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:260)
 ... 3 filtered
 at java.lang.reflect.Method.invoke(Method.java:498)
 at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:22)
 at com.sun.proxy.$Proxy14.reIndexAll(Unknown Source)
 at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:64)
 at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:48)
 at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.doReindex(ReIndexAsyncIndexerCommand.java:25)
 at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:54)
 at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.call(ReIndexAsyncIndexerCommand.java:16)
 at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:24)
 at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:458)
 at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:426)
 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:216)
 at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: read past EOF
 at org.apache.lucene.store.MMapDirectory$MMapIndexInput.readByte(MMapDirectory.java:278)
 at org.apache.lucene.store.ChecksumIndexInput.readByte(ChecksumIndexInput.java:40)
 at org.apache.lucene.store.DataInput.readInt(DataInput.java:84)
 at org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:269)
 at org.apache.lucene.index.IndexFileDeleter.<init>(IndexFileDeleter.java:168)
 at com.atlassian.jira.index.DefaultIndexEngine.clean(DefaultIndexEngine.java:176)
 ... 26 more
2018-05-11 16:57:07,404 JiraTaskExectionThread-1 INFO admin 1017x106x1 w6vum4 my-ipaddress /secure/admin/IndexReIndex.jspa [c.a.j.w.a.admin.index.IndexAdminImpl] Re-indexing finished
2018-05-11 16:57:07,404 JiraTaskExectionThread-1 ERROR admin 1017x106x1 w6vum4 my-ipaddress /secure/admin/IndexReIndex.jspa [c.a.jira.task.TaskManagerImpl] Task 'JIRA Indexing' failed.

[Andy Heinzer · Accepted solution]

Hi @Kaboya

It looks like your indexes are corrupted.   Try these steps:

Attempt to perform a full reindex of JIRA. If this is not possible as exceptions are thrown when attempting to reindex and it prevents it, follow the below instructions.

1. Stop JIRA

2. Make a backup of the following directory and all its sub-directories:

   $JIRA_HOME/caches/indexes

3. Remove that directory and all its sub-directories:

   $JIRA_HOME/caches/indexes

    This will be rebuilt when JIRA is re-indexed

4. Start JIRA
5. Perform a locked/full re-index of JIRA

There is also a KB on this specific problem in Unable to rebuild JIRA application indexes. That is where I pulled those steps from.    If you are unsure where your $JIRAHOME directory is, please see JIRA application home directory.  Following those steps should allow you to correct this problem.

[Kaboya]

This worked! Thanks. 

[forlooper]

Awesome! Thank you!

[LiveOrDevTrying]

Wow!!! What a life saver!! Tysm for posting this!

- Rob

[Priyanka Badugu]

Pheww.... This worked for me. Thanks!