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Jira reindex Timed out

invinci
invinci May 11, 2017

Hi,

I am trying to setup a second staging server for JIRA based on my current setup. I cloned the configurations, files and made all the connections to start JIRA, and it worked out fine. Now when I am trying to reindex, the prgoress stays at 0% for a long time and the log includes a repetitive stack trace. So I had to stop the reindexing, force jira to stop and restart again. I do not see any problem, so I go ahead adn do one more reindexing only to realize that the indexing is locked.


Here is the stack trace form the log:

2017-05-11 13:55:07,654 IssueIndexer:thread-2 DEBUG admin-sboddu 671x177x1 gb43he 10.20.20.253 /secure/admin/jira/IndexReIndex.jspa [c.o.scriptrunner.customfield.GroovyCustomField] com.atlassian.jira.issue.index.SearchUnavailableException
2017-05-11 13:55:07,655 IssueIndexer:thread-9 ERROR admin-sboddu 671x177x1 gb43he 10.20.20.253 /secure/admin/jira/IndexReIndex.jspa [c.a.j.issue.index.DefaultIndexManager] Wait attempt timed out - waited 30000 milliseconds
com.atlassian.jira.issue.index.IndexException: Wait attempt timed out - waited 30000 milliseconds
        at com.atlassian.jira.issue.index.DefaultIndexManager.obtain(DefaultIndexManager.java:794)
        at com.atlassian.jira.issue.index.DefaultIndexManager.access$600(DefaultIndexManager.java:88)
        at com.atlassian.jira.issue.index.DefaultIndexManager$IndexLock.tryLock(DefaultIndexManager.java:1118)
        at com.atlassian.jira.issue.index.DefaultIndexManager.getIndexLock(DefaultIndexManager.java:780)
        at com.atlassian.jira.issue.index.DefaultIndexManager.getEntitySearcher(DefaultIndexManager.java:847)
        at com.atlassian.jira.issue.index.DefaultIndexManager.getIssueSearcher(DefaultIndexManager.java:828)
        ... 2 filtered
        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:25)
        at com.sun.proxy.$Proxy13.getIssueSearcher(Unknown Source)
        at com.atlassian.jira.issue.search.SearchProviderFactoryImpl.getSearcher(SearchProviderFactoryImpl.java:18)
        at com.atlassian.jira.issue.search.providers.LuceneSearchProvider.search(LuceneSearchProvider.java:278)
        at com.atlassian.jira.issue.search.providers.LuceneSearchProvider.search(LuceneSearchProvider.java:91)
        at com.atlassian.jira.issue.search.providers.LuceneSearchProvider.search(LuceneSearchProvider.java:87)
        at com.atlassian.jira.bc.issue.search.DefaultSearchService.search(DefaultSearchService.java:111)
        at com.atlassian.jira.bc.issue.search.SearchService$search$2.call(Unknown Source)
        at Script4.runJQLSearch(Script4.groovy:106)
        ... 2 filtered
        at java.lang.reflect.Method.invoke(Method.java:497)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
        at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:151)
        at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl$2.invokeMethod(GroovyScriptEngineImpl.java:336)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:84)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:174)
        at Script4.retrieveIssuesInEpic(Script4.groovy:70)
        ... 2 filtered
        at java.lang.reflect.Method.invoke(Method.java:497)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
        at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:151)
        at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl$2.invokeMethod(GroovyScriptEngineImpl.java:336)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:84)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
        at Script4.run(Script4.groovy:38)
        at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:352)
        at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:153)
        at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:233)
        at javax.script.ScriptEngine$eval.call(Unknown Source)
        at com.onresolve.scriptrunner.runner.ScriptRunnerImpl.runScriptAndGetContext(ScriptRunnerImpl.groovy:156)
        at com.onresolve.scriptrunner.runner.ScriptRunner$runScriptAndGetContext$5.callCurrent(Unknown Source)
        at com.onresolve.scriptrunner.runner.ScriptRunnerImpl.runStringAsScript(ScriptRunnerImpl.groovy:144)
        at com.onresolve.scriptrunner.runner.ScriptRunner$runStringAsScript$4.call(Unknown Source)
        at com.onresolve.scriptrunner.customfield.GroovyCustomField.getValueFromIssue(GroovyCustomField.groovy:248)
        at com.atlassian.jira.issue.fields.CustomFieldImpl.getValue(CustomFieldImpl.java:386)
        at com.atlassian.jira.issue.index.indexers.impl.SortableTextCustomFieldIndexer.addDocumentFields(SortableTextCustomFieldIndexer.java:39)
        at com.atlassian.jira.issue.index.indexers.impl.SortableTextCustomFieldIndexer.addDocumentFieldsNotSearchable(SortableTextCustomFieldIndexer.java:34)
        at com.atlassian.jira.issue.index.indexers.impl.AbstractCustomFieldIndexer.addIndex(AbstractCustomFieldIndexer.java:42)
        at com.atlassian.jira.issue.index.DefaultIssueDocumentFactory$Builder.add(DefaultIssueDocumentFactory.java:88)
        at com.atlassian.jira.issue.index.DefaultIssueDocumentFactory$Builder.addAll(DefaultIssueDocumentFactory.java:79)
        at com.atlassian.jira.issue.index.DefaultIssueDocumentFactory.apply(DefaultIssueDocumentFactory.java:54)
        at com.atlassian.jira.issue.index.DefaultIssueDocumentFactory.apply(DefaultIssueDocumentFactory.java:34)
        at com.atlassian.jira.issue.index.DefaultIssueIndexer$DefaultDocumentCreationStrategy.get(DefaultIssueIndexer.java:553)
        at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:377)
        at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:366)
        at com.atlassian.jira.issue.index.DefaultIssueIndexer.lambda$null$2(DefaultIssueIndexer.java:305)
        at com.atlassian.jira.issue.index.DefaultIssueIndexer$$Lambda$354/1964386317.get(Unknown Source)
        at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:7)
        at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:5)
        at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:33)
        at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:31)
        at com.atlassian.jira.util.concurrent.BoundedExecutor$2.call(BoundedExecutor.java:68)
        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)
2017-05-11 13:55:07,656 IssueIndexer:thread-9 DEBUG admin-sboddu 671x177x1 gb43he 10.20.20.253 /secure/admin/jira/IndexReIndex.jspa [c.o.scriptrunner.customfield.GroovyCustomField] com.atlassian.jira.issue.index.SearchUnavailableException
2017-05-11 13:55:07,664 IssueIndexer:thread-8 ERROR admin-sboddu 671x177x1 gb43he 10.20.20.253 /secure/admin/jira/IndexReIndex.jspa [c.a.j.issue.index.DefaultIndexManager] Wait attempt timed out - waited 30000 milliseconds
com.atlassian.jira.issue.index.IndexException: Wait attempt timed out - waited 30000 milliseconds
        at com.atlassian.jira.issue.index.DefaultIndexManager.obtain(DefaultIndexManager.java:794)
        at com.atlassian.jira.issue.index.DefaultIndexManager.access$600(DefaultIndexManager.java:88)
        at com.atlassian.jira.issue.index.DefaultIndexManager$IndexLock.tryLock(DefaultIndexManager.java:1118)
        at com.atlassian.jira.issue.index.DefaultIndexManager.getIndexLock(DefaultIndexManager.java:780)
        at com.atlassian.jira.issue.index.DefaultIndexManager.getEntitySearcher(DefaultIndexManager.java:847)
        at com.atlassian.jira.issue.index.DefaultIndexManager.getIssueSearcher(DefaultIndexManager.java:828)
        ... 2 filtered
        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:25)
        at com.sun.proxy.$Proxy13.getIssueSearcher(Unknown Source)
        at com.atlassian.jira.issue.search.SearchProviderFactoryImpl.getSearcher(SearchProviderFactoryImpl.java:18)
        at com.atlassian.jira.issue.search.providers.LuceneSearchProvider.search(LuceneSearchProvider.java:278)
        at com.atlassian.jira.issue.search.providers.LuceneSearchProvider.search(LuceneSearchProvider.java:91)
        at com.atlassian.jira.issue.search.providers.LuceneSearchProvider.search(LuceneSearchProvider.java:87)
        at com.atlassian.jira.bc.issue.search.DefaultSearchService.search(DefaultSearchService.java:111)
        at com.atlassian.jira.bc.issue.search.SearchService$search$2.call(Unknown Source)
        at Script4.runJQLSearch(Script4.groovy:106)
        ... 2 filtered
        at java.lang.reflect.Method.invoke(Method.java:497)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
        at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:151)
        at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl$2.invokeMethod(GroovyScriptEngineImpl.java:336)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:84)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:174)
        at Script4.retrieveIssuesInEpic(Script4.groovy:70)
        ... 2 filtered
        at java.lang.reflect.Method.invoke(Method.java:497)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1212)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1021)
        at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:151)
        at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl$2.invokeMethod(GroovyScriptEngineImpl.java:336)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:84)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
        at Script4.run(Script4.groovy:38)
        at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:352)
        at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:153)
        at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:233)
        at javax.script.ScriptEngine$eval.call(Unknown Source)
        at com.onresolve.scriptrunner.runner.ScriptRunnerImpl.runScriptAndGetContext(ScriptRunnerImpl.groovy:156)
        at com.onresolve.scriptrunner.runner.ScriptRunner$runScriptAndGetContext$5.callCurrent(Unknown Source)
        at com.onresolve.scriptrunner.runner.ScriptRunnerImpl.runStringAsScript(ScriptRunnerImpl.groovy:144)
        at com.onresolve.scriptrunner.runner.ScriptRunner$runStringAsScript$4.call(Unknown Source)
        at com.onresolve.scriptrunner.customfield.GroovyCustomField.getValueFromIssue(GroovyCustomField.groovy:248)
        at com.atlassian.jira.issue.fields.CustomFieldImpl.getValue(CustomFieldImpl.java:386)
        at com.atlassian.jira.issue.index.indexers.impl.SortableTextCustomFieldIndexer.addDocumentFields(SortableTextCustomFieldIndexer.java:39)
        at com.atlassian.jira.issue.index.indexers.impl.SortableTextCustomFieldIndexer.addDocumentFieldsNotSearchable(SortableTextCustomFieldIndexer.java:34)
        at com.atlassian.jira.issue.index.indexers.impl.AbstractCustomFieldIndexer.addIndex(AbstractCustomFieldIndexer.java:42)
        at com.atlassian.jira.issue.index.DefaultIssueDocumentFactory$Builder.add(DefaultIssueDocumentFactory.java:88)
        at com.atlassian.jira.issue.index.DefaultIssueDocumentFactory$Builder.addAll(DefaultIssueDocumentFactory.java:79)
        at com.atlassian.jira.issue.index.DefaultIssueDocumentFactory.apply(DefaultIssueDocumentFactory.java:54)
        at com.atlassian.jira.issue.index.DefaultIssueDocumentFactory.apply(DefaultIssueDocumentFactory.java:34)
        at com.atlassian.jira.issue.index.DefaultIssueIndexer$DefaultDocumentCreationStrategy.get(DefaultIssueIndexer.java:553)
        at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:377)
        at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:366)
        at com.atlassian.jira.issue.index.DefaultIssueIndexer.lambda$null$2(DefaultIssueIndexer.java:305)
        at com.atlassian.jira.issue.index.DefaultIssueIndexer$$Lambda$354/1964386317.get(Unknown Source)
        at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:7)
        at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:5)
        at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:33)
        at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:31)
        at com.atlassian.jira.util.concurrent.BoundedExecutor$2.call(BoundedExecutor.java:68)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)

I believe this error is caused due to either one of the two problems:

1. As I tried to stop the initial reindex, the whole jira instance became non-responsive and it is unable to get out from the locked state ( even after I restart jira). 

2. I strongly believe that one of my custom field has failed and it is causing this error. The stack trace points to a Scripted Field (highlighted fields in the above log) that is custom to our workflow setup.

 

Please let me know how to diagnose this issue.

Thank You!

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Daniel Yelamos [Adaptavist]
Daniel Yelamos [Adaptavist]
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May 19, 2017

Hello Invinci:

This looks like a known error from the Lucene index. You can find more information about how to fix it here

Could you give us your Jira version? We would like to attempt to reproduce this.

Cheers!

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