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Jira Service Desk shuts down sporadically after scheduling an upgrade Edited

We are running Service Desk 8.1 Server as Linux service on Ubuntu 18.04. 

From time to time the service fails immediately after start up or later in the day. The last thing seen in logs then is an Upgrade Scheduler starting and re-indexing. 

On the days when the service doesn't fail after "Upgrade", the version stays still 8.1. So these updates don't seem to have any effect.

Please provide guidance to fix this failure.

How can I prevent the Update Scheduler starting on the daily basis at all? I cannot see any setting for it and don't want any automatic updates.

VM args:

/opt/atlassian/jira/jre//bin/java -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms1024m -Xmx1024m -XX:InitialCodeCacheSize=32m -XX:ReservedCodeCacheSize=512m -Djava.awt.headless=true -Datlassian.standalone=JIRA -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory -XX:-OmitStackTraceInFastThrow -Djava.locale.providers=COMPAT -Djira.home=/var/atlassian/application-data/jira -Datlassian.plugins.startup.options= -Djdk.tls.ephemeralDHKeySize=2048 -Djava.protocol.handler.pkgs=org.apache.catalina.webresources -Dorg.apache.catalina.security.SecurityListener.UMASK=0027 -Xloggc:/opt/atlassian/jira/logs/atlassian-jira-gc-%t.log -XX:+UseGCLogFileRotation -XX:NumberOfGCLogFiles=5 -XX:GCLogFileSize=20M -XX:+PrintGCDetails -XX:+PrintGCDateStamps -XX:+PrintGCTimeStamps -XX:+PrintGCCause -Dignore.endorsed.dirs= -classpath /opt/atlassian/jira/bin/bootstrap.jar:/opt/atlassian/jira/bin/tomcat-juli.jar -Dcatalina.base=/opt/atlassian/jira -Dcatalina.home=/opt/atlassian/jira -Djava.io.tmpdir=/opt/atlassian/jira/temp org.apache.catalina.startup.Bootstrap start

 

Logs from failing "Upgrade" are below:

2019-09-10 08:02:53,017 JIRA-Bootstrap INFO      [c.a.jira.upgrade.UpgradeScheduler] Scheduling upgrades to run in 1 minute(s)
2019-09-10 08:02:56,543 JIRA-Bootstrap INFO      [c.a.jira.startup.LauncherContextListener] Memory Usage:
    ---------------------------------------------------------------------------------
      Heap memory     :  Used:  632 MiB.  Committed:  981 MiB.  Max:  987 MiB
      Non-heap memory :  Used:  274 MiB.  Committed:  301 MiB.  Max: 1536 MiB
    ---------------------------------------------------------------------------------
      TOTAL           :  Used:  906 MiB.  Committed: 1282 MiB.  Max: 2523 MiB
    ---------------------------------------------------------------------------------
2019-09-10 08:02:57,218 Caesium-1-3 INFO      [c.a.jira.startup.IndexRecoveryLauncher] Running start-index-recovery
2019-09-10 08:02:57,344 Caesium-1-1 INFO ServiceRunner     [c.a.jira.startup.CacheWarmerLauncher] Warming up 3 caches.
2019-09-10 08:02:57,794 Caesium-1-3 INFO      [c.a.jira.startup.IndexRecoveryLauncher] Indexing issues from=2019-08-29 11:11:07.0 to=Thu Aug 29 11:11:07 CEST 2019 (time span of 666ms)
2019-09-10 08:03:00,813 Caesium-1-3 INFO      [c.a.jira.startup.IndexRecoveryLauncher] Progress=60%, task=Recovering, message=Recovered added and updated issues
2019-09-10 08:03:00,914 Caesium-1-3 INFO      [c.a.jira.startup.IndexRecoveryLauncher] Progress=80%, task=Recovering, message=Cleaned removed issues
2019-09-10 08:03:00,914 Caesium-1-3 INFO      [c.a.jira.startup.IndexRecoveryLauncher] Finished start-index-recovery
2019-09-10 08:03:05,655 Modification Check:thread-1 INFO      [c.a.jira.startup.JiraStartupLogger]    ___ Modifications ___________________________         Modified Files                                : jira-application.properties
         Removed Files                                 : None10-Sep-2019 08:03:17.767 INFO [Thread-4] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
10-Sep-2019 08:03:17.779 INFO [Thread-4] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
2019-09-10 08:03:18,525 localhost-startStop-2 INFO      [c.a.jira.startup.DefaultJiraLauncher] Stopping launchers
2019-09-10 08:03:26,167 Caesium-1-1 INFO ServiceRunner     [c.a.jira.startup.CacheWarmerLauncher] Warmed cache(s) in 28813 ms.
2019-09-10 08:03:50,976 localhost-startStop-2 INFO      [c.a.jira.startup.DefaultJiraLauncher] JIRA launchers stopped in 32449ms
10-Sep-2019 08:03:51.091 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [service-desk] appears to have started a thread named [JonasBatch] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.lang.Object.wait(Object.java:502)

....

Logs from a successful "Upgrade":

2019-08-12 08:02:51,467 JIRA-Bootstrap INFO      [c.a.jira.upgrade.UpgradeScheduler] Scheduling upgrades to run in 1 minute(s)
2019-08-12 08:02:54,958 JIRA-Bootstrap INFO      [c.a.jira.startup.LauncherContextListener] Memory Usage:
    ---------------------------------------------------------------------------------
      Heap memory     :  Used:  593 MiB.  Committed:  999 MiB.  Max:  999 MiB
      Non-heap memory :  Used:  274 MiB.  Committed:  302 MiB.  Max: 1536 MiB
    ---------------------------------------------------------------------------------
      TOTAL           :  Used:  868 MiB.  Committed: 1300 MiB.  Max: 2535 MiB
    ---------------------------------------------------------------------------------
2019-08-12 08:02:55,321 Caesium-1-1 INFO ServiceRunner     [c.a.jira.startup.IndexRecoveryLauncher] Running start-index-recovery
2019-08-12 08:02:55,340 Caesium-1-4 INFO      [c.a.jira.startup.CacheWarmerLauncher] Warming up 3 caches.
2019-08-12 08:02:56,673 Caesium-1-1 INFO ServiceRunner     [c.a.jira.startup.IndexRecoveryLauncher] Indexing issues from=2019-08-07 15:23:02.0 to=Wed Aug 07 15:23:02 CEST 2019 (time span of 32ms)
2019-08-12 08:02:58,840 Caesium-1-1 INFO ServiceRunner     [c.a.jira.startup.IndexRecoveryLauncher] Progress=60%, task=Recovering, message=Recovered added and updated issues
2019-08-12 08:02:58,910 Caesium-1-1 INFO ServiceRunner     [c.a.jira.startup.IndexRecoveryLauncher] Progress=80%, task=Recovering, message=Cleaned removed issues
2019-08-12 08:02:58,910 Caesium-1-1 INFO ServiceRunner     [c.a.jira.startup.IndexRecoveryLauncher] Finished start-index-recovery
2019-08-12 08:03:08,300 Modification Check:thread-1 INFO      [c.a.jira.startup.JiraStartupLogger]    ___ Modifications ___________________________         Modified Files                                : jira-application.properties
         Removed Files                                 : None2019-08-12 08:03:21,091 Caesium-1-4 INFO      [c.a.jira.startup.CacheWarmerLauncher] Warmed cache(s) in 25728 ms.
2019-08-12 08:03:51,471 Caesium-1-2 INFO ServiceRunner     [c.a.jira.upgrade.UpgradeScheduler] Running scheduled upgrades
2019-08-12 08:03:51,475 Caesium-1-2 INFO ServiceRunner     [c.a.jira.upgrade.LoggingUpgradeService] run upgrades has started
2019-08-12 08:03:51,544 Caesium-1-2 INFO ServiceRunner     [c.a.j.upgrade.util.BuildNumberDao] Setting current build number to 801000
2019-08-12 08:03:51,569 Caesium-1-2 INFO ServiceRunner     [c.a.jira.upgrade.UpgradeIndexManager] There is no reindex requests of type [IMMEDIATE, DELAYED] so none will be run
2019-08-12 08:03:51,569 Caesium-1-2 INFO ServiceRunner     [c.a.j.upgrade.util.BuildNumberDao] Setting current version to 8.1.0
2019-08-12 08:03:51,590 Caesium-1-2 INFO ServiceRunner     [c.a.j.upgrade.util.BuildNumberDao] Setting downgrade version to 7.1.2
2019-08-12 08:03:51,623 Caesium-1-2 INFO ServiceRunner     [c.a.jira.upgrade.LoggingUpgradeService] run upgrades has finished successfully, and took 148 milliseconds to process.
2019-08-12 08:03:51,623 Caesium-1-2 INFO ServiceRunner     [c.a.jira.upgrade.UpgradeScheduler] JIRA upgrades completed successfully
2019-08-12 08:03:51,649 Caesium-1-2 INFO ServiceRunner     [c.a.jira.upgrade.UpgradeScheduler] Plugins upgrades completed successfully
2019-08-12 08:03:51,651 Caesium-1-2 INFO ServiceRunner     [c.a.jira.upgrade.UpgradeIndexManager] Reindexing is not allowed after this upgrade and there is no immediate reindex requests

 

 

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