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Deadlock with HashMap and ScripRunner

Mike Wells
Mike Wells
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June 18, 2015

I updated from JIRA 6.3.7 to 6.4.6, when I start JIRA I get the following exception...

2015-06-18 11:43:17,183 DeadlockDetection:thread-1 ERROR      [atlassian.jira.startup.LauncherContextListener] A deadlock has been detected on JIRA startup for the following threads: ["Thread-34" Id=100 BLOCKED on java.util.HashMap@4c9460af owned by "localhost-startStop-1" Id=13, "localhost-startStop-1" Id=13 BLOCKED on groovy.util.GroovyScriptEngine$ScriptClassLoader@cedc0af owned by "Thread-34" Id=100]
2015-06-18 11:43:17,185 DeadlockDetection:thread-1 ERROR      [atlassian.jira.startup.LauncherContextListener] "Thread-34" Id=100 BLOCKED on java.util.HashMap@4c9460af owned by "localhost-startStop-1" Id=13
    at groovy.lang.GroovyClassLoader.recompile(GroovyClassLoader.java:735)
    -  blocked on java.util.HashMap@4c9460af
    at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:696)
    at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:765)
    at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:753)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Unknown Source)
    at java_lang_Class$forName$1.call(Unknown Source)
    at com.onresolve.scriptrunner.runner.ScriptRunnerImpl.loadScriptByName(ScriptRunnerImpl.groovy:583)
    ...:
    groovy.lang.GroovyClassLoader.recompile(GroovyClassLoader.java:735)
    groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:696)
    groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:765)
    groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:753)
    java.lang.Class.forName0(Native Method)
    java.lang.Class.forName(Unknown Source)
    java_lang_Class$forName$1.call(Unknown Source)
    com.onresolve.scriptrunner.runner.ScriptRunnerImpl.loadScriptByName(ScriptRunnerImpl.groovy:583)
    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    java.lang.reflect.Method.invoke(Unknown Source)
    org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)
    groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:324)
    org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:368)
    groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1016)
    org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:66)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:145)
    com.onresolve.scriptrunner.runner.ScriptRunnerImpl$_listScripts_closure8_closure11.doCall(ScriptRunnerImpl.groovy:650)
    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    java.lang.reflect.Method.invoke(Unknown Source)
    org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)
    groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:324)
    org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:278)
    groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1016)
    groovy.lang.Closure.call(Closure.java:423)
    groovy.lang.Closure.call(Closure.java:439)
    org.codehaus.groovy.runtime.ResourceGroovyMethods.eachFileRecurse(ResourceGroovyMethods.java:1099)
    org.codehaus.groovy.runtime.ResourceGroovyMethods.eachFileRecurse(ResourceGroovyMethods.java:1331)
    org.codehaus.groovy.runtime.dgm$792.invoke(Unknown Source)
    org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:271)
    org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:53)
    org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
    com.onresolve.scriptrunner.runner.ScriptRunnerImpl$_listScripts_closure8.doCall(ScriptRunnerImpl.groovy:639)
    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    java.lang.reflect.Method.invoke(Unknown Source)
    org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)
    groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:324)
    org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:278)
    groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1016)
    groovy.lang.Closure.call(Closure.java:423)
    groovy.lang.Closure.call(Closure.java:439)
    org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:1379)
    org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:1372)
    org.codehaus.groovy.runtime.dgm$149.invoke(Unknown Source)
    org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:271)
    org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:53)
    org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
    com.onresolve.scriptrunner.runner.ScriptRunnerImpl.listScripts(ScriptRunnerImpl.groovy:636)
    com.onresolve.scriptrunner.runner.ScriptRunnerImpl.listScriptsSuppressErrors(ScriptRunnerImpl.groovy:618)
    com.onresolve.scriptrunner.runner.ScriptRunnerImpl.listScriptsSuppressErrors(ScriptRunnerImpl.groovy)
    com.onresolve.scriptrunner.runner.ScriptRunner$listScriptsSuppressErrors$0.call(Unknown Source)
    org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
    com.onresolve.scriptrunner.runner.JqlFunctionsManagerImpl.registerScriptedJqlFunctions(JqlFunctionsManagerImpl.groovy:198)
    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    java.lang.reflect.Method.invoke(Unknown Source)
    org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)
    groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:324)
    groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1207)
    org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnCurrentN(ScriptBytecodeAdapter.java:78)
    com.onresolve.scriptrunner.runner.JqlFunctionsManagerImpl.this$dist$invoke$1(JqlFunctionsManagerImpl.groovy)
    com.onresolve.scriptrunner.runner.JqlFunctionsManagerImpl$RegisterJqlFunctions.methodMissing(JqlFunctionsManagerImpl.groovy)
    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    java.lang.reflect.Method.invoke(Unknown Source)
    org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)
    groovy.lang.MetaClassImpl.invokeMissingMethod(MetaClassImpl.java:933)
    groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1256)
    groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1209)
    groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1016)
    org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:66)
    org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:49)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:137)
    com.onresolve.scriptrunner.runner.JqlFunctionsManagerImpl$RegisterJqlFunctions.run(JqlFunctionsManagerImpl.groovy:270)
    java.lang.Thread.run(Unknown Source)
2015-06-18 11:43:17,186 DeadlockDetection:thread-1 ERROR      [atlassian.jira.startup.LauncherContextListener] "localhost-startStop-1" Id=13 BLOCKED on groovy.util.GroovyScriptEngine$ScriptClassLoader@cedc0af owned by "Thread-34" Id=100
    at java.lang.ClassLoader.loadClass(Unknown Source)
    -  blocked on groovy.util.GroovyScriptEngine$ScriptClassLoader@cedc0af
    at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:655)
    at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:523)
    at org.codehaus.groovy.control.ClassNodeResolver.tryAsLoaderClassOrScript(ClassNodeResolver.java:183)
    at org.codehaus.groovy.control.ClassNodeResolver.findClassNode(ClassNodeResolver.java:168)
    at groovy.util.GroovyScriptEngine$ScriptClassLoader$3.findClassNode(GroovyScriptEngine.java:218)
    at org.codehaus.groovy.control.ClassNodeResolver.resolveName(ClassNodeResolver.java:124)
    at org.codehaus.groovy.control.ResolveVisitor.resolveToOuter(ResolveVisitor.java:617)
    ...:
    java.lang.ClassLoader.loadClass(Unknown Source)
    groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:655)
    groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:523)
    org.codehaus.groovy.control.ClassNodeResolver.tryAsLoaderClassOrScript(ClassNodeResolver.java:183)
    org.codehaus.groovy.control.ClassNodeResolver.findClassNode(ClassNodeResolver.java:168)
    groovy.util.GroovyScriptEngine$ScriptClassLoader$3.findClassNode(GroovyScriptEngine.java:218)
    org.codehaus.groovy.control.ClassNodeResolver.resolveName(ClassNodeResolver.java:124)
    org.codehaus.groovy.control.ResolveVisitor.resolveToOuter(ResolveVisitor.java:617)
    org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:269)
    org.codehaus.groovy.control.ResolveVisitor.resolveFromDefaultImports(ResolveVisitor.java:397)
    org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:269)
    org.codehaus.groovy.control.ResolveVisitor.resolveFromStaticInnerClasses(ResolveVisitor.java:372)
    org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:269)
    org.codehaus.groovy.control.ResolveVisitor.resolveFromStaticInnerClasses(ResolveVisitor.java:372)
    org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:269)
    org.codehaus.groovy.control.ResolveVisitor.resolveFromStaticInnerClasses(ResolveVisitor.java:372)
    org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:269)
    org.codehaus.groovy.control.ResolveVisitor.resolveFromStaticInnerClasses(ResolveVisitor.java:372)
    org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:269)
    org.codehaus.groovy.control.ResolveVisitor.resolveFromStaticInnerClasses(ResolveVisitor.java:372)
    org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:269)
    org.codehaus.groovy.control.ResolveVisitor.resolveFromStaticInnerClasses(ResolveVisitor.java:372)
    org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:269)
    org.codehaus.groovy.control.ResolveVisitor.visitClass(ResolveVisitor.java:1159)
    org.codehaus.groovy.control.ResolveVisitor.startResolving(ResolveVisitor.java:142)
    org.codehaus.groovy.control.CompilationUnit$11.call(CompilationUnit.java:643)
    org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:923)
    org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:585)
    org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:534)
    groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:286)
    groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:259)
    groovy.util.GroovyScriptEngine$ScriptClassLoader.doParseClass(GroovyScriptEngine.java:267)
    groovy.util.GroovyScriptEngine$ScriptClassLoader.parseClass(GroovyScriptEngine.java:236)
    groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:245)
    groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:203)
    groovy.util.GroovyScriptEngine.loadScriptByName(GroovyScriptEngine.java:540)
    groovy.util.GroovyScriptEngine.createScript(GroovyScriptEngine.java:590)
    groovy.util.GroovyScriptEngine.run(GroovyScriptEngine.java:577)
    groovy.util.GroovyScriptEngine$run$2.call(Unknown Source)
    org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:120)
    com.onresolve.scriptrunner.runner.ScriptRunnerImpl.runScript(ScriptRunnerImpl.groovy:403)
    com.onresolve.scriptrunner.runner.ScriptRunner$runScript$4.callCurrent(Unknown Source)
    org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:49)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:145)
    com.onresolve.scriptrunner.runner.ScriptRunnerImpl.runFileAsScript(ScriptRunnerImpl.groovy:182)
    com.onresolve.scriptrunner.runner.ScriptRunner$runFileAsScript$2.call(Unknown Source)
    org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
    org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:120)
    com.onresolve.scriptrunner.customfield.GroovyCustomField.getValueFromIssue(GroovyCustomField.groovy:144)
    com.atlassian.jira.issue.fields.CustomFieldImpl.getValue(CustomFieldImpl.java:454)
    com.atlassian.jira.issue.index.indexers.impl.SortableTextCustomFieldIndexer.addDocumentFields(SortableTextCustomFieldIndexer.java:44)
    com.atlassian.jira.issue.index.indexers.impl.SortableTextCustomFieldIndexer.addDocumentFieldsSearchable(SortableTextCustomFieldIndexer.java:33)
    com.atlassian.jira.issue.index.indexers.impl.AbstractCustomFieldIndexer.addIndex(AbstractCustomFieldIndexer.java:46)
    com.atlassian.jira.issue.index.DefaultIssueDocumentFactory$Builder.add(DefaultIssueDocumentFactory.java:102)
    com.atlassian.jira.issue.index.DefaultIssueDocumentFactory$Builder.addAll(DefaultIssueDocumentFactory.java:91)
    com.atlassian.jira.issue.index.DefaultIssueDocumentFactory.apply(DefaultIssueDocumentFactory.java:60)
    com.atlassian.jira.issue.index.DefaultIssueDocumentFactory.apply(DefaultIssueDocumentFactory.java:37)
    com.atlassian.jira.issue.index.DefaultIssueIndexer$DefaultDocumentCreationStrategy.get(DefaultIssueIndexer.java:644)
    com.atlassian.jira.issue.index.DefaultIssueIndexer$2.perform(DefaultIssueIndexer.java:182)
    com.atlassian.jira.issue.index.DefaultIssueIndexer$2.perform(DefaultIssueIndexer.java:175)
    com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:334)
    com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:330)
    com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:9)
    com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:5)
    com.atlassian.jira.issue.index.DefaultIssueIndexer$3.consume(DefaultIssueIndexer.java:329)
    com.atlassian.jira.issue.index.DefaultIssueIndexer$3.consume(DefaultIssueIndexer.java:321)
    com.atlassian.jira.issue.util.DatabaseIssuesIterable.foreach(DatabaseIssuesIterable.java:66)
    com.atlassian.jira.issue.index.DefaultIssueIndexer.perform(DefaultIssueIndexer.java:320)
    com.atlassian.jira.issue.index.DefaultIssueIndexer.reindexIssues(DefaultIssueIndexer.java:174)
    com.atlassian.jira.index.ha.DefaultIndexRecoveryManager.reindexUsingDatabaseLatest(DefaultIndexRecoveryManager.java:202)
    com.atlassian.jira.index.ha.DefaultIndexRecoveryManager.reindexIssuesIn(DefaultIndexRecoveryManager.java:173)
    com.atlassian.jira.startup.IndexRecoveryLauncher.start(IndexRecoveryLauncher.java:71)
    com.atlassian.jira.startup.DefaultJiraLauncher$3.run(DefaultJiraLauncher.java:143)
    com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:345)
    com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:215)
    com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:124)
    com.atlassian.jira.startup.DefaultJiraLauncher.access$100(DefaultJiraLauncher.java:33)
    com.atlassian.jira.startup.DefaultJiraLauncher$1.run(DefaultJiraLauncher.java:86)
    com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:34)
    com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:81)
    com.atlassian.jira.startup.LauncherContextListener.contextInitialized(LauncherContextListener.java:72)
    org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4992)
    org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5490)
    org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1575)
    org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1565)
    java.util.concurrent.FutureTask.run(Unknown Source)
    java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    java.lang.Thread.run(Unknown Source)

 

It seems to be related to a deadlock between HashMap and ScriptRunner.

I found the documentation for this problem, https://confluence.atlassian.com/display/JIRAKB/Deadlock+detected+on+startup+error+in+logfile, but the resolutions are not working for me. Restarting doesn't help.

To further compound the issues I can't simply role back to the previous version of JIRA as it is now incompaitble with the DB.

Any ideas of a solution?

 

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Mike Wells
Mike Wells
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June 18, 2015

Not too sure what the problem was, but I removed the script runner plugin from the installed-plugins folder and replaced it with the latest version. JIRA started fine after that.

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Mike Wells
Mike Wells
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June 18, 2015

I had 3.0.6 installed, not JDK8 perhaps. Anyway I removed that one and replaced it with 3.0.16. JIRA started this time. I have some fresh errors in one of my scripted JQL functions, but I suspect this is a different issue. I will open another question on that one if the issue persists.

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JamieA
JamieA
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June 18, 2015

That's no good... what version of the plugin? Does it happen repeatedly? If so you may have to remove it from installed-plugins, if it's blocking you from starting jira and this is not a staging instance.

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