java.io.IOException: read past EOF

zimbra.com | 6 months ago
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  1. 0

    IOException: read past EOF

    GitHub | 2 years ago | kjlubick
    java.io.IOException: read past EOF
  2. 0

    We had a case where Nexus was stopped (not cleanly shutdown) due to a physical machine reboot. When trying to bring the service back up the exception below was thrown in the logs. The resolution was to delete the Lucene index at /sonatype-work/nexus/timeline and then the server started correctly. 2009-03-25 11:05:53.743 ERROR [WrapperListener_start_runner:] - org.mortbay.log: Failed startup of context org.mortbay.jetty.webapp.WebAppContext@ee260b{/repo,../../../runtime/apps/nexus/webapp} java.lang.IllegalStateException: Could not initialize Nexus. at org.sonatype.nexus.web.NexusBooterListener.contextInitialized(NexusBooterListener.java:45) at org.mortbay.jetty.handler.ContextHandler.startContext(ContextHandler.java:548) at org.mortbay.jetty.servlet.Context.startContext(Context.java:136) at org.mortbay.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1234) at org.mortbay.jetty.handler.ContextHandler.doStart(ContextHandler.java:517) at org.mortbay.jetty.webapp.WebAppContext.doStart(WebAppContext.java:460) at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50) at org.mortbay.jetty.handler.HandlerCollection.doStart(HandlerCollection.java:152) at org.mortbay.jetty.handler.ContextHandlerCollection.doStart(ContextHandlerCollection.java:156) at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50) at org.mortbay.jetty.handler.HandlerWrapper.doStart(HandlerWrapper.java:130) at org.mortbay.jetty.Server.doStart(Server.java:222) at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50) at org.sonatype.plexus.jetty.DefaultServletContainer.start(DefaultServletContainer.java:312) at org.codehaus.plexus.personality.plexus.lifecycle.phase.StartPhase.execute(StartPhase.java:33) at org.codehaus.plexus.lifecycle.AbstractLifecycleHandler.start(AbstractLifecycleHandler.java:97) at org.codehaus.plexus.component.builder.XBeanComponentBuilder.startComponentLifecycle(XBeanComponentBuilder.java:220) at org.codehaus.plexus.component.builder.XBeanComponentBuilder.build(XBeanComponentBuilder.java:98) at org.codehaus.plexus.component.manager.AbstractComponentManager.createComponentInstance(AbstractComponentManager.java:135) at org.codehaus.plexus.component.manager.ClassicSingletonComponentManager.getComponent(ClassicSingletonComponentManager.java:96) at org.codehaus.plexus.DefaultComponentLookupManager.lookup(DefaultComponentLookupManager.java:147) at org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:484) at org.codehaus.plexus.container.initialization.StartLoadOnStartComponentsPhase.execute(StartLoadOnStartComponentsPhase.java:69) at org.codehaus.plexus.DefaultPlexusContainer.initializePhases(DefaultPlexusContainer.java:849) at org.codehaus.plexus.DefaultPlexusContainer.initialize(DefaultPlexusContainer.java:813) at org.codehaus.plexus.DefaultPlexusContainer.construct(DefaultPlexusContainer.java:405) at org.codehaus.plexus.DefaultPlexusContainer.<init>(DefaultPlexusContainer.java:196) at org.sonatype.appbooter.PlexusContainerHost.startContainer(PlexusContainerHost.java:280) at org.sonatype.appbooter.jsw.PlexusJSWListener.start(PlexusJSWListener.java:99) at org.tanukisoftware.wrapper.WrapperManager$12.run(WrapperManager.java:2788) Caused by: org.codehaus.plexus.component.repository.exception.ComponentLookupException: Unable to lookup component 'org.sonatype.nexus.Nexus', it could not be started. role: org.sonatype.nexus.Nexus roleHint: default classRealm: plexus at org.codehaus.plexus.DefaultComponentLookupManager.lookup(DefaultComponentLookupManager.java:155) at org.codehaus.plexus.DefaultComponentLookupManager.lookup(DefaultComponentLookupManager.java:69) at org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:430) at org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:424) at org.sonatype.nexus.web.NexusBooterListener.contextInitialized(NexusBooterListener.java:39) ... 29 more Caused by: org.codehaus.plexus.component.repository.exception.ComponentLifecycleException: Error starting component at org.codehaus.plexus.component.builder.XBeanComponentBuilder.startComponentLifecycle(XBeanComponentBuilder.java:222) at org.codehaus.plexus.component.builder.XBeanComponentBuilder.build(XBeanComponentBuilder.java:98) at org.codehaus.plexus.component.manager.AbstractComponentManager.createComponentInstance(AbstractComponentManager.java:135) at org.codehaus.plexus.component.manager.ClassicSingletonComponentManager.getComponent(ClassicSingletonComponentManager.java:96) at org.codehaus.plexus.DefaultComponentLookupManager.lookup(DefaultComponentLookupManager.java:147) ... 33 more Caused by: org.codehaus.plexus.personality.plexus.lifecycle.phase.PhaseExecutionException: Error starting component at org.codehaus.plexus.personality.plexus.lifecycle.phase.StartPhase.execute(StartPhase.java:37) at org.codehaus.plexus.lifecycle.AbstractLifecycleHandler.start(AbstractLifecycleHandler.java:97) at org.codehaus.plexus.component.builder.XBeanComponentBuilder.startComponentLifecycle(XBeanComponentBuilder.java:220) ... 37 more Caused by: org.codehaus.plexus.personality.plexus.lifecycle.phase.StartingException: Could not start Nexus! at org.sonatype.nexus.DefaultNexus.start(DefaultNexus.java:1564) at org.codehaus.plexus.personality.plexus.lifecycle.phase.StartPhase.execute(StartPhase.java:33) ... 39 more Caused by: org.codehaus.plexus.personality.plexus.lifecycle.phase.StartingException: Cannot start Timeline! at org.sonatype.nexus.timeline.DefaultTimeline.startService(DefaultTimeline.java:173) at org.sonatype.nexus.feeds.DefaultFeedRecorder.startService(DefaultFeedRecorder.java:101) at org.sonatype.nexus.DefaultNexus.startService(DefaultNexus.java:1600) at org.sonatype.nexus.DefaultNexus.start(DefaultNexus.java:1560) ... 40 more Caused by: java.io.IOException: read past EOF at org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:146) at org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:38) at org.apache.lucene.store.IndexInput.readInt(IndexInput.java:66) at org.apache.lucene.store.IndexInput.readLong(IndexInput.java:89) at org.apache.lucene.index.SegmentInfo.<init>(SegmentInfo.java:140) at org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:220) at org.apache.lucene.index.SegmentInfos$1.doBody(SegmentInfos.java:254) at org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:636) at org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:251) at org.apache.lucene.index.IndexWriter.init(IndexWriter.java:710) at org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:614) at org.sonatype.nexus.index.context.NexusIndexWriter.<init>(NexusIndexWriter.java:35) at org.sonatype.nexus.timeline.DefaultTimeline.startService(DefaultTimeline.java:155) ... 43 more

    Sonatype JIRA | 8 years ago | Eric Dalquist
    java.lang.IllegalStateException: Could not initialize Nexus.
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  4. 0

    Confluence runs as root. The index is in the data directory. Exception is as follows: {code} 2008-06-23 16:14:06,183 Thread-21 ERROR com.atlassian.confluence.ext.usage.event.UsageEventListener Error indexing task: UsageEventWrapperTask: view:page(20217860) at Mon Jun 23 16:14:04 JST 2008: com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF at com.atlassian.bonnie.LuceneConnection.createAndConfigureWriter(LuceneConnection.java:338) at com.atlassian.bonnie.LuceneConnection.getWriter(LuceneConnection.java:433) at com.atlassian.bonnie.LuceneConnection.withWriter(LuceneConnection.java:246) at com.atlassian.bonnie.LuceneConnection.withWriter(LuceneConnection.java:237) at com.atlassian.confluence.ext.usage.index.UsageIndexManager.index(UsageIndexManager.java:206) at com.atlassian.confluence.ext.usage.event.UsageEventListener$1.run(UsageEventListener.java:71) at EDU.oswego.cs.dl.util.concurrent.QueuedExecutor$RunLoop.run(QueuedExecutor.java:89) at java.lang.Thread.run(Thread.java:619) Caused by: java.io.IOException: read past EOF at org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:137) at org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:38) at org.apache.lucene.store.IndexInput.readInt(IndexInput.java:47) at org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:200) at org.apache.lucene.index.SegmentInfos$1.doBody(SegmentInfos.java:246) at org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:610) at org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:243) at org.apache.lucene.index.IndexWriter.init(IndexWriter.java:616) at org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:410) at com.atlassian.bonnie.LuceneConnection.createAndConfigureWriter(LuceneConnection.java:332) ... 7 more {code}

    Atlassian JIRA | 9 years ago | Dimitar Dimitrov
    com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF
  5. 0

    We had a case where Nexus was stopped (not cleanly shutdown) due to a physical machine reboot. When trying to bring the service back up the exception below was thrown in the logs. The resolution was to delete the Lucene index at /sonatype-work/nexus/timeline and then the server started correctly. 2009-03-25 11:05:53.743 ERROR [WrapperListener_start_runner:] - org.mortbay.log: Failed startup of context org.mortbay.jetty.webapp.WebAppContext@ee260b{/repo,../../../runtime/apps/nexus/webapp} java.lang.IllegalStateException: Could not initialize Nexus. at org.sonatype.nexus.web.NexusBooterListener.contextInitialized(NexusBooterListener.java:45) at org.mortbay.jetty.handler.ContextHandler.startContext(ContextHandler.java:548) at org.mortbay.jetty.servlet.Context.startContext(Context.java:136) at org.mortbay.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1234) at org.mortbay.jetty.handler.ContextHandler.doStart(ContextHandler.java:517) at org.mortbay.jetty.webapp.WebAppContext.doStart(WebAppContext.java:460) at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50) at org.mortbay.jetty.handler.HandlerCollection.doStart(HandlerCollection.java:152) at org.mortbay.jetty.handler.ContextHandlerCollection.doStart(ContextHandlerCollection.java:156) at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50) at org.mortbay.jetty.handler.HandlerWrapper.doStart(HandlerWrapper.java:130) at org.mortbay.jetty.Server.doStart(Server.java:222) at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50) at org.sonatype.plexus.jetty.DefaultServletContainer.start(DefaultServletContainer.java:312) at org.codehaus.plexus.personality.plexus.lifecycle.phase.StartPhase.execute(StartPhase.java:33) at org.codehaus.plexus.lifecycle.AbstractLifecycleHandler.start(AbstractLifecycleHandler.java:97) at org.codehaus.plexus.component.builder.XBeanComponentBuilder.startComponentLifecycle(XBeanComponentBuilder.java:220) at org.codehaus.plexus.component.builder.XBeanComponentBuilder.build(XBeanComponentBuilder.java:98) at org.codehaus.plexus.component.manager.AbstractComponentManager.createComponentInstance(AbstractComponentManager.java:135) at org.codehaus.plexus.component.manager.ClassicSingletonComponentManager.getComponent(ClassicSingletonComponentManager.java:96) at org.codehaus.plexus.DefaultComponentLookupManager.lookup(DefaultComponentLookupManager.java:147) at org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:484) at org.codehaus.plexus.container.initialization.StartLoadOnStartComponentsPhase.execute(StartLoadOnStartComponentsPhase.java:69) at org.codehaus.plexus.DefaultPlexusContainer.initializePhases(DefaultPlexusContainer.java:849) at org.codehaus.plexus.DefaultPlexusContainer.initialize(DefaultPlexusContainer.java:813) at org.codehaus.plexus.DefaultPlexusContainer.construct(DefaultPlexusContainer.java:405) at org.codehaus.plexus.DefaultPlexusContainer.<init>(DefaultPlexusContainer.java:196) at org.sonatype.appbooter.PlexusContainerHost.startContainer(PlexusContainerHost.java:280) at org.sonatype.appbooter.jsw.PlexusJSWListener.start(PlexusJSWListener.java:99) at org.tanukisoftware.wrapper.WrapperManager$12.run(WrapperManager.java:2788) Caused by: org.codehaus.plexus.component.repository.exception.ComponentLookupException: Unable to lookup component 'org.sonatype.nexus.Nexus', it could not be started. role: org.sonatype.nexus.Nexus roleHint: default classRealm: plexus at org.codehaus.plexus.DefaultComponentLookupManager.lookup(DefaultComponentLookupManager.java:155) at org.codehaus.plexus.DefaultComponentLookupManager.lookup(DefaultComponentLookupManager.java:69) at org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:430) at org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:424) at org.sonatype.nexus.web.NexusBooterListener.contextInitialized(NexusBooterListener.java:39) ... 29 more Caused by: org.codehaus.plexus.component.repository.exception.ComponentLifecycleException: Error starting component at org.codehaus.plexus.component.builder.XBeanComponentBuilder.startComponentLifecycle(XBeanComponentBuilder.java:222) at org.codehaus.plexus.component.builder.XBeanComponentBuilder.build(XBeanComponentBuilder.java:98) at org.codehaus.plexus.component.manager.AbstractComponentManager.createComponentInstance(AbstractComponentManager.java:135) at org.codehaus.plexus.component.manager.ClassicSingletonComponentManager.getComponent(ClassicSingletonComponentManager.java:96) at org.codehaus.plexus.DefaultComponentLookupManager.lookup(DefaultComponentLookupManager.java:147) ... 33 more Caused by: org.codehaus.plexus.personality.plexus.lifecycle.phase.PhaseExecutionException: Error starting component at org.codehaus.plexus.personality.plexus.lifecycle.phase.StartPhase.execute(StartPhase.java:37) at org.codehaus.plexus.lifecycle.AbstractLifecycleHandler.start(AbstractLifecycleHandler.java:97) at org.codehaus.plexus.component.builder.XBeanComponentBuilder.startComponentLifecycle(XBeanComponentBuilder.java:220) ... 37 more Caused by: org.codehaus.plexus.personality.plexus.lifecycle.phase.StartingException: Could not start Nexus! at org.sonatype.nexus.DefaultNexus.start(DefaultNexus.java:1564) at org.codehaus.plexus.personality.plexus.lifecycle.phase.StartPhase.execute(StartPhase.java:33) ... 39 more Caused by: org.codehaus.plexus.personality.plexus.lifecycle.phase.StartingException: Cannot start Timeline! at org.sonatype.nexus.timeline.DefaultTimeline.startService(DefaultTimeline.java:173) at org.sonatype.nexus.feeds.DefaultFeedRecorder.startService(DefaultFeedRecorder.java:101) at org.sonatype.nexus.DefaultNexus.startService(DefaultNexus.java:1600) at org.sonatype.nexus.DefaultNexus.start(DefaultNexus.java:1560) ... 40 more Caused by: java.io.IOException: read past EOF at org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:146) at org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:38) at org.apache.lucene.store.IndexInput.readInt(IndexInput.java:66) at org.apache.lucene.store.IndexInput.readLong(IndexInput.java:89) at org.apache.lucene.index.SegmentInfo.<init>(SegmentInfo.java:140) at org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:220) at org.apache.lucene.index.SegmentInfos$1.doBody(SegmentInfos.java:254) at org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:636) at org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:251) at org.apache.lucene.index.IndexWriter.init(IndexWriter.java:710) at org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:614) at org.sonatype.nexus.index.context.NexusIndexWriter.<init>(NexusIndexWriter.java:35) at org.sonatype.nexus.timeline.DefaultTimeline.startService(DefaultTimeline.java:155) ... 43 more

    Sonatype JIRA | 8 years ago | Eric Dalquist
    java.lang.IllegalStateException: Could not initialize Nexus.

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    Root Cause Analysis

    1. java.io.IOException

      read past EOF

      at org.apache.lucene.store.BufferedIndexInput.refill()
    2. Lucene
      IndexWriter.<init>
      1. org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:223)
      2. org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:39)
      3. org.apache.lucene.store.DataInput.readInt(DataInput.java:84)
      4. org.apache.lucene.store.BufferedIndexInput.readInt(BufferedIndexInput.java:169)
      5. org.apache.lucene.index.FieldsReader.detectCodeVersion(FieldsReader.java:91)
      6. org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:303)
      7. org.apache.lucene.index.SegmentInfos$1.doBody(SegmentInfos.java:363)
      8. org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:754)
      9. org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:593)
      10. org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:359)
      11. org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:1148)
      11 frames
    3. com.zimbra.cs
      MailboxIndex$IndexTask.run
      1. com.zimbra.cs.index.LuceneIndex$4.<init>(LuceneIndex.java:318)
      2. com.zimbra.cs.index.LuceneIndex.openIndexWriter(LuceneIndex.java:318)
      3. com.zimbra.cs.index.LuceneIndex.openWriter(LuceneIndex.java:485)
      4. com.zimbra.cs.index.LuceneIndex.openIndexer(LuceneIndex.java:470)
      5. com.zimbra.cs.mailbox.MailboxIndex.add(MailboxIndex.java:880)
      6. com.zimbra.cs.mailbox.Mailbox.endTransaction(Mailbox.java:8555)
      7. com.zimbra.cs.mailbox.MailboxIndex.indexItemList(MailboxIndex.java:763)
      8. com.zimbra.cs.mailbox.MailboxIndex.indexDeferredItems(MailboxIndex.java:373)
      9. com.zimbra.cs.mailbox.MailboxIndex.access$600(MailboxIndex.java:83)
      10. com.zimbra.cs.mailbox.MailboxIndex$BatchIndexTask.exec(MailboxIndex.java:1404)
      11. com.zimbra.cs.mailbox.MailboxIndex$IndexTask.run(MailboxIndex.java:1383)
      11 frames
    4. Java RT
      Thread.run
      1. java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
      2. java.util.concurrent.FutureTask.run(FutureTask.java:262)
      3. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
      4. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
      5. java.lang.Thread.run(Thread.java:744)
      5 frames