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?
