Unable to stop Jira

[Seemi Anwar]

Hi Experts,

I want to upgrade Jira , but I am unable to stop Jira.  Following is the current status of Jira. Could anyone please guide me?

jira.service
Loaded: loaded (/etc/init.d/jira; generated)
Active: active (exited) since Thu 2020-09-10 14:41:02 UTC; 1h 32min ago
Docs: man:systemd-sysv-generator(8)
Process: 17212 ExecStop=/etc/init.d/jira stop (code=exited, status=1/FAILURE)
Process: 17547 ExecStart=/etc/init.d/jira start (code=exited, status=0/SUCCESS)

Sep 10 14:41:02 jira[17547]: Atlassian Jira
Sep 10 14:41:02  jira[17547]: Version : 8.10.0
Sep 10 14:41:02 jira[17547]: [19B blob data]
Sep 10 14:41:02  jira[17547]: If you encounter issues starting or stopping Jira, please see the Troubleshooting guide at https://docs.atlassian.com/jira/
Sep 10 14:41:02  jira[17547]: Server startup logs are located in /opt/atlassian/jira/logs/catalina.out
Sep 10 14:41:02  jira[17547]: Existing PID file found during start.
Sep 10 14:41:02 jira[17547]: Removing/clearing stale PID file.
Sep 10 14:41:02 jira[17547]: Tomcat started.
Sep 10 14:41:02  runuser[17565]: pam_unix(runuser:session): session closed for user jira
Sep 10 14:41:02  systemd[1]: Started jira.service.

[Nic Brough -Adaptavist-]

How are you trying to stop Jira and what is the output of that?

[Seemi Anwar]

I am using the command "sudo service Jira stop" to stop the server. It's not giving me any output.  But the Jira software (GUI Application on Web) is still running. 

[Nic Brough -Adaptavist-]

If there's no output from that, it means the service controller script got no output back from the Jira shut-down script.

That is not that unusual, a lot of applications (yes, Java, I'm looking at you for failing to enforce output on failure) don't feed back in a way that service control scripts understand, which is incredibly annoying, but something we admins are stuck with and have to deal with.

The next things to read are:

• <jira install>/logs/catalina.out
• <jira home>/log/atlassian-jira.log

One of those two will probably have an error message in there telling you that it got a shutdown message and why it did not do it.

[Seemi Anwar]

HI, I got this information when i opened atlassian-jira.log . Will this information help us?

2020-09-09 10:46:19,413+0000 index-writer-stats-ISSUE-2-0 INFO      [c.a.jira.index.WriterWithStats] [index-writer-stats] ISSUE : total stats: {"addDocumentsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"deleteDocumentsMillis":{"count":8,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentConditionallyMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentsWithVersionMillis":{"count":1,"min":804,"max":804,"sum":804,"avg":804,"distributionCounter":{"10":0,"100":0,"500":0,"1000":1,"5000":0,"10000":0,"30000":0,"60000":0}},"updateDocumentsWithVersionSize":{"count":1,"min":1,"max":1,"sum":1,"avg":1,"distributionCounter":{"1":1,"10":0,"100":0,"1000":0,"10000":0}},"replaceDocumentsWithVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"10":0,"100":0,"500":0,"1000":0,"5000":0,"10000":0,"30000":0,"60000":0}},"replaceDocumentsWithVersionSize":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"1":0,"10":0,"100":0,"1000":0,"10000":0}},"optimizeMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"closeMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"commitMillis":{"count":1,"min":244,"max":244,"sum":244,"avg":244,"distributionCounter":{}}}

2020-09-09 10:46:19,414+0000 index-writer-stats-ISSUE-2-0 INFO      [c.a.jira.index.WriterWithStats] [index-writer-stats] ISSUE : snapshot stats: {"addDocumentsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"deleteDocumentsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentConditionallyMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentsWithVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"10":0,"100":0,"500":0,"1000":0,"5000":0,"10000":0,"30000":0,"60000":0}},"updateDocumentsWithVersionSize":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"1":0,"10":0,"100":0,"1000":0,"10000":0}},"replaceDocumentsWithVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"10":0,"100":0,"500":0,"1000":0,"5000":0,"10000":0,"30000":0,"60000":0}},"replaceDocumentsWithVersionSize":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"1":0,"10":0,"100":0,"1000":0,"10000":0}},"optimizeMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"closeMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"commitMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}}}

2020-09-09 10:46:20,926+0000 index-writer-stats-WORKLOG-3-0 INFO      [c.a.jira.index.WriterWithStats] [index-writer-stats] WORKLOG : total stats: {"addDocumentsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"deleteDocumentsMillis":{"count":8,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentsMillis":{"count":1,"min":5,"max":5,"sum":5,"avg":5,"distributionCounter":{}},"updateDocumentConditionallyMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentsWithVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"10":0,"100":0,"500":0,"1000":0,"5000":0,"10000":0,"30000":0,"60000":0}},"updateDocumentsWithVersionSize":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"1":0,"10":0,"100":0,"1000":0,"10000":0}},"replaceDocumentsWithVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"10":0,"100":0,"500":0,"1000":0,"5000":0,"10000":0,"30000":0,"60000":0}},"replaceDocumentsWithVersionSize":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"1":0,"10":0,"100":0,"1000":0,"10000":0}},"optimizeMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"closeMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"commitMillis":{"count":1,"min":33,"max":33,"sum":33,"avg":33,"distributionCounter":{}}}

2020-09-09 10:46:20,927+0000 index-writer-stats-WORKLOG-3-0 INFO      [c.a.jira.index.WriterWithStats] [index-writer-stats] WORKLOG : snapshot stats: {"addDocumentsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"deleteDocumentsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentConditionallyMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentsWithVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"10":0,"100":0,"500":0,"1000":0,"5000":0,"10000":0,"30000":0,"60000":0}},"updateDocumentsWithVersionSize":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"1":0,"10":0,"100":0,"1000":0,"10000":0}},"replaceDocumentsWithVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"10":0,"100":0,"500":0,"1000":0,"5000":0,"10000":0,"30000":0,"60000":0}},"replaceDocumentsWithVersionSize":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"1":0,"10":0,"100":0,"1000":0,"10000":0}},"optimizeMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"closeMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"commitMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}}}

2020-09-09 10:47:06,633+0000 PlatformInstrumentsLoggingService RUNNING WARN      [c.a.j.cache.request.RequestCacheImpl] Incorrect usage of JIRA API. You can only create/use: RequestCacheImpl inside a context (request or Jira-Thread-Local). Check: JiraThreadLocalUtil for details.

2020-09-09 10:47:06,633+0000 PlatformInstrumentsLoggingService RUNNING WARN      [c.a.j.cache.request.RequestCacheImpl] From Jira 9.0 version creation/usage of RequestCacheImpl will throw the IllegalStateException.

2020-09-09 10:47:06,633+0000 PlatformInstrumentsLoggingService RUNNING WARN      [c.a.j.cache.request.RequestCacheImpl] Incorrect usage of JIRA API. You can only create/use: RequestCacheImpl inside a context (request or Jira-Thread-Local). Check: JiraThreadLocalUtil for details.

2020-09-09 10:47:06,633+0000 PlatformInstrumentsLoggingService RUNNING WARN      [c.a.j.cache.request.RequestCacheImpl] From Jira 9.0 version creation/usage of RequestCa

[Seemi Anwar]

When i opened catalina.out. I got this information. 

15-Jul-2020 14:32:04.531 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/8.5.50
15-Jul-2020 14:32:04.533 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Dec 7 2019 19:19:46 UTC
15-Jul-2020 14:32:04.533 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 8.5.50.0
15-Jul-2020 14:32:04.533 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
15-Jul-2020 14:32:04.536 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 4.15.0-1052-aws
15-Jul-2020 14:32:04.536 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
15-Jul-2020 14:32:04.537 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /opt/atlassian/jira/jre
15-Jul-2020 14:32:04.537 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_202-b08
15-Jul-2020 14:32:04.537 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
15-Jul-2020 14:32:04.538 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /opt/atlassian/jira
15-Jul-2020 14:32:04.538 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /opt/atlassian/jira
15-Jul-2020 14:32:04.540 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties
15-Jul-2020 14:32:04.541 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
15-Jul-2020 14:32:04.541 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms384m
15-Jul-2020 14:32:04.541 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx2048m
15-Jul-2020 14:32:04.542 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:InitialCodeCacheSize=32m
15-Jul-2020 14:32:04.542 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:ReservedCodeCacheSize=512m
15-Jul-2020 14:32:04.542 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
15-Jul-2020 14:32:04.542 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.standalone=JIRA
15-Jul-2020 14:32:04.543 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true
15-Jul-2020 14:32:04.543 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dmail.mime.decodeparameters=true
15-Jul-2020 14:32:04.543 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
15-Jul-2020 14:32:04.544 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow
15-Jul-2020 14:32:04.544 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.locale.providers=COMPAT
15-Jul-2020 14:32:04.544 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.plugins.startup.options=
15-Jul-2020 14:32:04.544 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
15-Jul-2020 14:32:04.545 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
15-Jul-2020 14:32:04.545 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
15-Jul-2020 14:32:04.545 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xloggc:/opt/atlassian/jira/logs/atlassian-jira-gc-%t.log
15-Jul-2020 14:32:04.546 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+UseGCLogFileRotation
15-Jul-2020 14:32:04.546 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:NumberOfGCLogFiles=5
15-Jul-2020 14:32:04.546 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:GCLogFileSize=20M
15-Jul-2020 14:32:04.546 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDetails
15-Jul-2020 14:32:04.547 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDateStamps
15-Jul-2020 14:32:04.547 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCTimeStamps
15-Jul-2020 14:32:04.548 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCCause
catalina.out

[Nic Brough -Adaptavist-]

These logs show no shutdown message being recieved and no fatal process-ending errors.  So either it is running, or something in your operating system is killing it.

[Seemi Anwar]

Hi, when I used the command "sudo /etc/init.d/jira stop" to stop Jira, I got the following error message "PID file found but either no matching process was found or the current user does not have permission to stop the process. Stop aborted". Is this message giving us any hint to resolve the issue? 

Server startup logs are located in /opt/atlassian/jira/logs/catalina.out
Using CATALINA_BASE: /opt/atlassian/jira
Using CATALINA_HOME: /opt/atlassian/jira
Using CATALINA_TMPDIR: /opt/atlassian/jira/temp
Using JRE_HOME: /opt/atlassian/jira/jre/
Using CLASSPATH: /opt/atlassian/jira/bin/bootstrap.jar:/opt/atlassian/jira /bin/tomcat-juli.jar
Using CATALINA_PID: /opt/atlassian/jira/work/catalina.pid
PID file found but either no matching process was found or the current user does not have permission to stop the process. Stop aborted.

[Nic Brough -Adaptavist-]

That message effectively says that it's not running at all.

[Seemi Anwar]

could you please help me what should I do to stop Jira? 

[Nic Brough -Adaptavist-]

Seeing as you're using three different stop and start methods and have two different reports on whether it is running or not, then I'm afraid I can only say that you've got your startup/shutdown into a mess.

So:

• Check if Jira is running by hand - ignore the scripts.
  • ps -ef | grep -i jira
• If this returns a huge long command line with a load of paths and -XX, -D and CATALINA stuff in it, then Jira is running.  That line will also have contained the process id as the second column, so you can then run
  • kill -9 <process id>
• Give it a few seconds, then retry the ps command.  You may need to be "root", and you might need to give it a bit more than a few seconds if it's really behaving badly
• Now decide whether you want to use systemd or init.d to control it
• Delete the method you don't want (rename or move the systemd unit file, or stick an "exit" right at the top of the init.d script)
• Check the permissions and ownership on your Jira installation and Jira data directories - they and all their content should be owned by the jira user
• Swap to use the jira user
• Go you your Jira installation/bin (given your original question, I'd say /opt/atlassian/jira/bin and run ./start-jira.sh
• Test Jira and make sure it's running ok.  You can then plumb it into your chosen start up script.