This is similar to the issue here: https://confluence.atlassian.com/display/JIRAKB/JIRA+startup+failed+or+JIRA+not+Functioning+due+to+IllegalStateException+zip+file+closed+error?utm_source=STP&utm_medium=logScan
but occurs on shutdown. Is the resolution the same?
2015-02-24 07:08:24,627 localhost-startStop-2 ERROR [osgi.container.felix.FelixOsgiContainerManager] JarContent: Unable to read bytes.
java.lang.IllegalStateException: zip file closed
at java.util.zip.ZipFile.ensureOpen(Unknown Source)
at java.util.zip.ZipFile.getEntry(Unknown Source)
at java.util.jar.JarFile.getEntry(Unknown Source)
at org.apache.felix.framework.util.JarFileX.getEntry(JarFileX.java:61)
at org.apache.felix.framework.cache.JarContent.getEntryAsBytes(JarContent.java:120)
at org.apache.felix.framework.ModuleImpl$ModuleClassLoader.findClass(ModuleImpl.java:1738)
at org.apache.felix.framework.ModuleImpl.findClassOrResourceByDelegation(ModuleImpl.java:716)
at org.apache.felix.framework.ModuleImpl.access$200(ModuleImpl.java:73)
at org.apache.felix.framework.ModuleImpl$ModuleClassLoader.loadClass(ModuleImpl.java:1690)
at java.lang.ClassLoader.loadClass(Unknown Source)
at java.lang.Class.getDeclaringClass0(Native Method)
at java.lang.Class.getDeclaringClass(Unknown Source)
at java.lang.Class.getEnclosingClass(Unknown Source)
at java.lang.Class.getCanonicalName(Unknown Source)
at com.atlassian.threadlocal.BruteForceThreadLocalCleanup.getPrettyClassName(BruteForceThreadLocalCleanup.java:257)
at com.atlassian.threadlocal.BruteForceThreadLocalCleanup.checkThreadLocalMapForLeaks(BruteForceThreadLocalCleanup.java:181)
at com.atlassian.threadlocal.BruteForceThreadLocalCleanup.cleanUpThreadImpl(BruteForceThreadLocalCleanup.java:135)
at com.atlassian.threadlocal.BruteForceThreadLocalCleanup.cleanupThreadLocals(BruteForceThreadLocalCleanup.java:94)
at com.atlassian.threadlocal.BruteForceThreadLocalCleanup.cleanUp(BruteForceThreadLocalCleanup.java:63)
at com.atlassian.jira.startup.DefaultJiraLauncher.cleanupThreadLocals(DefaultJiraLauncher.java:192)
at com.atlassian.jira.startup.DefaultJiraLauncher.cleanupAfterOurselves(DefaultJiraLauncher.java:173)
at com.atlassian.jira.startup.DefaultJiraLauncher.stop(DefaultJiraLauncher.java:168)
at com.atlassian.jira.startup.LauncherContextListener.contextDestroyed(LauncherContextListener.java:112) <+5> (StandardContext.java:5033) (StandardContext.java:5685) (LifecycleBase.java:232) (ContainerBase.java:1591) (ContainerBase.java:1580)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
2015-02-24 07:11:14,822 localhost-startStop-1 INFO [atlassian.jira.startup.JiraStartupLogger]
The errors do seem to line up between what you're seeing and the knowledge base article, so I would definitely recommend running through the resolutions listed in the article. As Andris said, it's likely that the problem shares a similar root cause, despite the behavior being slightly different than what is described in the article.
Almost certainly it's the same.
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