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PID file found but no matching process was found. Stop aborted.

[root@server bin]# ./stop-confluence.sh
executing as current user
If you encounter issues starting up Confluence, please see the Installation guide at http://confluence.atlassian.com/display/DOC/Confluence+Installation+Guide

Server startup logs are located in /home/user/atlassian/confluence/logs/catalina.out
Using CATALINA_BASE:   /home/user/atlassian/confluence
Using CATALINA_HOME:   /home/iuser/atlassian/confluence
Using CATALINA_TMPDIR: /home/user/atlassian/confluence/temp
Using JRE_HOME:        /home/user/atlassian/confluence/jre/
Using CLASSPATH:       /home/user/atlassian/confluence/bin/bootstrap.jar:/home/izaapinn/atlassian/confluence/bin/tomcat-juli.jar
Using CATALINA_PID:    /home/user/atlassian/confluence/work/catalina.pid
PID file found but no matching process was found. Stop aborted.

2 answers

0 votes
Daniel Eads Atlassian Team Nov 17, 2018

Hey Kannan,

This happens sometimes if there were issues starting up (or shutting down cleanly). Looks like the stop process thinks that Confluence is already stopped.

You can check if Confluence is still running by looking for a matching Java process in ps:

ps aux | grep confluence

At this point if you find one, you could kill it with the kill -9 command. Otherwise you should be alright to start Confluence back up.

Cheers,
Daniel 

Hi daniel,

 

             Thanks alot please check with command output

 

[root@server ~]# ps aux | grep confluence
root     14401  0.0  0.0 103316   892 pts/1    S+   18:02   0:00 grep confluence

Like wenbo han likes this

[root@server ~]# ps aux | grep confluence
root     14401  0.0  0.0 103316   892 pts/1    S+   18:02   0:00 grep confluence
[root@server ~]# ^C
[root@server ~]# kill -9 14401
-bash: kill: (14401) - No such process
[root@server ~]# kill -9 103316
-bash: kill: (103316) - No such process
[root@server ~]#

Daniel Eads Atlassian Team Nov 17, 2018

The process that returned was actually the search process! Sorry for not calling out to ignore that one. Had Confluence been running, you've have seen a java process (not just the grep one) with a lot of startup flags after it - that process would take a few lines of output.

Regarding backups - there are basically two things to think about:

  1. Confluence itself can write an xml backup on a schedule. I'm guessing this is what you've turned off. It's ok to turn this off if you've got a production-level backup plan in place for your system (see next point)
  2. We suggest backing up the file system on your application server and also using your database's backup tools to back up Confluence's database on a regular interval. Details on that are in this guide.

Hi daniel,

 

               Please look at it

 

[root@server bin]# ps -ef|grep confluence
root     14909 14831  0 18:18 pts/1    00:00:00 grep confluence
[root@server bin]# ps aux | grep confluence
root     14911  0.0  0.0 103316   888 pts/1    S+   18:18   0:00 grep confluence
[root@server bin]# kill -9 14911
bash: kill: (14911) - No such process
[root@server bin]# kill -9 14831
Killed
-bash-4.1$ whoami
user
-bash-4.1$ su
Password:
[root@server user]# pwd
/home/user
[root@server user]# cd /home/user/atlassian/confluence/bin/
[root@server bin]# ./start-confluence.sh

To run Confluence in the foreground, start the server with start-confluence.sh -                                                                                        fg
executing as current user
If you encounter issues starting up Confluence, please see the Installation guid                                                                                        e at http://confluence.atlassian.com/display/DOC/Confluence+Installation+Guide

Server startup logs are located in /home/user/atlassian/confluence/logs/cata                                                                                        lina.out
Using CATALINA_BASE:   /home/user/atlassian/confluence
Using CATALINA_HOME:   /home/user/atlassian/confluence
Using CATALINA_TMPDIR: /home/user/atlassian/confluence/temp
Using JRE_HOME:        /home/user/atlassian/confluence/jre/
Using CLASSPATH:       /home/user/atlassian/confluence/bin/bootstrap.jar:/ho                                                                                        me/user/atlassian/confluence/bin/tomcat-juli.jar
Using CATALINA_PID:    /home/user/atlassian/confluence/work/catalina.pid
Existing PID file found during start.
Removing/clearing stale PID file.
Tomcat started.
[root@server bin]# ./stop-confluence.sh
executing as current user
If you encounter issues starting up Confluence, please see the Installation guid                                                                                        e at http://confluence.atlassian.com/display/DOC/Confluence+Installation+Guide

Server startup logs are located in /home/user/atlassian/confluence/logs/cata                                                                                        lina.out
Using CATALINA_BASE:   /home/user/atlassian/confluence
Using CATALINA_HOME:   /home/user/atlassian/confluence
Using CATALINA_TMPDIR: /home/user/atlassian/confluence/temp
Using JRE_HOME:        /home/user/atlassian/confluence/jre/
Using CLASSPATH:       /home/user/atlassian/confluence/bin/bootstrap.jar:/ho                                                                                        me/user/atlassian/confluence/bin/tomcat-juli.jar
Using CATALINA_PID:    /home/user/atlassian/confluence/work/catalina.pid
Killing Tomcat with the PID: 14964
The Tomcat process has been killed.
[root@server bin]# ./start-confluence.sh

To run Confluence in the foreground, start the server with start-confluence.sh -                                                                                        fg
executing as current user
If you encounter issues starting up Confluence, please see the Installation guid                                                                                        e at http://confluence.atlassian.com/display/DOC/Confluence+Installation+Guide

Server startup logs are located in /home/user/atlassian/confluence/logs/cata                                                                                        lina.out
Using CATALINA_BASE:   /home/user/atlassian/confluence
Using CATALINA_HOME:   /home/user/atlassian/confluence
Using CATALINA_TMPDIR: /home/user/atlassian/confluence/temp
Using JRE_HOME:        /home/user/atlassian/confluence/jre/
Using CLASSPATH:       /home/user/atlassian/confluence/bin/bootstrap.jar:/ho                                                                                        me/user/atlassian/confluence/bin/tomcat-juli.jar
Using CATALINA_PID:    /home/user/atlassian/confluence/work/catalina.pid
Tomcat started.
[root@server bin]# ./stop-confluence.sh
executing as current user
If you encounter issues starting up Confluence, please see the Installation guide at http://confluence.atlassian.com/display/DOC/Confluence+Installation+Guide

Server startup logs are located in /home/user/atlassian/confluence/logs/catalina.out
Using CATALINA_BASE:   /home/user/atlassian/confluence
Using CATALINA_HOME:   /home/user/atlassian/confluence
Using CATALINA_TMPDIR: /home/user/atlassian/confluence/temp
Using JRE_HOME:        /home/user/atlassian/confluence/jre/
Using CLASSPATH:       /home/user/atlassian/confluence/bin/bootstrap.jar:/home/user/atlassian/confluence/bin/tomcat-juli.jar
Using CATALINA_PID:    /home/user/atlassian/confluence/work/catalina.pid
PID file found but no matching process was found. Stop aborted.
[root@server bin]#

Daniel Eads Atlassian Team Nov 17, 2018

Hey Kannan,

It looks like you were able to successfully start/stop Confluence once.

Then after that, you were able to run the startup script but the shutdown script right after that errorred out.

I'm going to assume that someone/thing else didn't kill the Confluence job between you starting and stopping it the second time. What likely happened is that there was some error during startup that prevented Confluence from launching all the way (and the process terminated before you ran the shutdown command).

More information on what happened during that startup will be in /home/user/atlassian/confluence/logs/catalina.out - take a look at the last startup there and see if any errors popped up.

Hi daniel,

 

            Please check with logs

 

 

2018-11-17 18:21:00,315 ERROR [localhost-startStop-1] [atlassian.config.bootstrap.DefaultAtlassianBootstrapManager] init Home is not configured properly:
com.atlassian.config.ConfigurationException: Failed to parse config file: Error on line 2 of document  : The processing instruction target matching "[xX][mM][lL]" is not allowed. Nested exception: The processing instruction target matching "[xX][mM][lL]" is not allowed.
        at com.atlassian.config.xml.DefaultDom4jXmlConfigurationPersister.load(DefaultDom4jXmlConfigurationPersister.java:35)
        at com.atlassian.config.xml.DefaultDom4jXmlConfigurationPersister.load(DefaultDom4jXmlConfigurationPersister.java:65)
        at com.atlassian.config.ApplicationConfig.load(ApplicationConfig.java:262)
        at com.atlassian.config.bootstrap.DefaultAtlassianBootstrapManager.init(DefaultAtlassianBootstrapManager.java:68)
        at com.atlassian.config.util.BootstrapUtils.init(BootstrapUtils.java:36)
        at com.atlassian.confluence.setup.ConfluenceConfigurationListener.initialiseBootstrapContext(ConfluenceConfigurationListener.java:129)
        at com.atlassian.confluence.setup.ConfluenceConfigurationListener.contextInitialized(ConfluenceConfigurationListener.java:64)
        at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4973)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5467)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1559)
        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1549)
        at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.lang.Thread.run(Unknown Source)
Caused by: org.dom4j.DocumentException: Error on line 2 of document  : The processing instruction target matching "[xX][mM][lL]" is not allowed. Nested exception: The processing instruction target matching "[xX][mM][lL]" is not allowed.
        at org.dom4j.io.SAXReader.read(SAXReader.java:355)
        at org.dom4j.io.SAXReader.read(SAXReader.java:261)
        at com.atlassian.config.xml.AbstractDom4jXmlConfigurationPersister.loadDocument(AbstractDom4jXmlConfigurationPersister.java:68)
        at com.atlassian.config.xml.DefaultDom4jXmlConfigurationPersister.load(DefaultDom4jXmlConfigurationPersister.java:31)
        ... 16 more
2018-11-17 18:21:00,384 ERROR [localhost-startStop-1] [atlassian.confluence.setup.ConfluenceConfigurationListener] contextInitialized An error was encountered while bootstrapping Confluence (see below):
Unable to bootstrap application: Failed to parse config file: Error on line 2 of document  : The processing instruction target matching "[xX][mM][lL]" is not allowed. Nested exception: The processing instruction target matching "[xX][mM][lL]" is not allowed.
com.atlassian.config.bootstrap.BootstrapException: Unable to bootstrap application: Failed to parse config file: Error on line 2 of document  : The processing instruction target matching "[xX][mM][lL]" is not allowed. Nested exception: The processing instruction target matching "[xX][mM][lL]" is not allowed.
                                                                                                                                                       at com.atlassian.config.util.BootstrapUtils.init(BootstrapUtils.java:39)
        at com.atlassian.confluence.setup.ConfluenceConfigurationListener.initialiseBootstrapContext(ConfluenceConfigurationListener.java:129)
        at com.atlassian.confluence.setup.ConfluenceConfigurationListener.contextInitialized(ConfluenceConfigurationListener.java:64)
        at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4973)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5467)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1559)
        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1549)
        at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.lang.Thread.run(Unknown Source)
2018-11-17 18:21:18,708 INFO [localhost-startStop-1] [com.atlassian.confluence.lifecycle] init Confluence is ready to serve
Nov 17, 2018 6:21:18 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8090"]
Nov 17, 2018 6:21:18 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 39751 ms
Nov 17, 2018 6:21:18 PM org.apache.catalina.core.StandardServer await
SEVERE: StandardServer.await: create[localhost:8090]:
java.net.BindException: Address already in use
        at java.net.PlainSocketImpl.socketBind(Native Method)
        at java.net.AbstractPlainSocketImpl.bind(Unknown Source)
        at java.net.ServerSocket.bind(Unknown Source)
        at java.net.ServerSocket.<init>(Unknown Source)
        at org.apache.catalina.core.StandardServer.await(StandardServer.java:426)
        at org.apache.catalina.startup.Catalina.await(Catalina.java:777)
        at org.apache.catalina.startup.Catalina.start(Catalina.java:723)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
        at java.lang.reflect.Method.invoke(Unknown Source)
        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:321)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:455)

Nov 17, 2018 6:21:18 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8090"]
Nov 17, 2018 6:21:18 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Tomcat-Standalone
2018-11-17 18:21:18,851 FATAL [localhost-startStop-1] [atlassian.spring.container.SpringContainerContext] getComponent Spring Application context has not been set
2018-11-17 18:21:18,940 WARN [localhost-startStop-1] [atlassian.confluence.plugin.PluginFrameworkContextListener] contextDestroyed Failed to shut down plugin system during ServletContext shutdown: Spring Application context has not been set
2018-11-17 18:21:18,941 INFO [localhost-startStop-1] [com.atlassian.confluence.lifecycle] contextDestroyed Stopping Confluence

Nov 17, 2018 6:21:19 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [] registered the JDBC driver [org.hsqldb.jdbc.JDBCDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Nov 17, 2018 6:21:19 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Nov 17, 2018 6:21:19 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [Abandoned connection cleanup thread] but has failed to stop it. This is very likely to create a memory leak.
Nov 17, 2018 6:21:19 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8090"]
Nov 17, 2018 6:21:19 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8090"]

       

 

 

 

 

 

 

 

 

at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.lang.Thread.run(Unknown Source)
Caused by: org.dom4j.DocumentException: Error on line 2 of document  : The processing instruction target matching "[xX][mM][lL]" is not allowed. Nested exception: The processing instruction target matching "[xX][mM][lL]" is not allowed.
        at org.dom4j.io.SAXReader.read(SAXReader.java:355)
        at org.dom4j.io.SAXReader.read(SAXReader.java:261)
        at com.atlassian.config.xml.AbstractDom4jXmlConfigurationPersister.loadDocument(AbstractDom4jXmlConfigurationPersister.java:68)
        at com.atlassian.config.xml.DefaultDom4jXmlConfigurationPersister.load(DefaultDom4jXmlConfigurationPersister.java:31)
        ... 16 more
2018-11-17 18:21:00,384 ERROR [localhost-startStop-1] [atlassian.confluence.setup.ConfluenceConfigurationListener] contextInitialized An error was encountered while bootstrapping Confluence (see below):
Unable to bootstrap application: Failed to parse config file: Error on line 2 of document  : The processing instruction target matching "[xX][mM][lL]" is not allowed. Nested exception: The processing instruction target matching "[xX][mM][lL]" is not allowed.
com.atlassian.config.bootstrap.BootstrapException: Unable to bootstrap application: Failed to parse config file: Error on line 2 of document  : The processing instruction target matching "[xX][mM][lL]" is not allowed. Nested exception: The processing instruction target matching "[xX][mM][lL]" is not allowed.
        at com.atlassian.config.util.BootstrapUtils.init(BootstrapUtils.java:39)
        at com.atlassian.confluence.setup.ConfluenceConfigurationListener.initialiseBootstrapContext(ConfluenceConfigurationListener.java:129)
        at com.atlassian.confluence.setup.ConfluenceConfigurationListener.contextInitialized(ConfluenceConfigurationListener.java:64)
        at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4973)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5467)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1559)
        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1549)
        at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
        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)
2018-11-17 18:21:18,708 INFO [localhost-startStop-1] [com.atlassian.confluence.lifecycle] init Confluence is ready to serve
Nov 17, 2018 6:21:18 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8090"]
Nov 17, 2018 6:21:18 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 39751 ms
Nov 17, 2018 6:21:18 PM org.apache.catalina.core.StandardServer await
SEVERE: StandardServer.await: create[localhost:8090]:
java.net.BindException: Address already in use
        at java.net.PlainSocketImpl.socketBind(Native Method)
        at java.net.AbstractPlainSocketImpl.bind(Unknown Source)
        at java.net.ServerSocket.bind(Unknown Source)
        at java.net.ServerSocket.<init>(Unknown Source)
        at org.apache.catalina.core.StandardServer.await(StandardServer.java:426)
        at org.apache.catalina.startup.Catalina.await(Catalina.java:777)

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Nov 17, 2018 6:21:18 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8090"]
Nov 17, 2018 6:21:18 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Tomcat-Standalone
2018-11-17 18:21:18,851 FATAL [localhost-startStop-1] [atlassian.spring.container.SpringContainerContext] getComponent Spring Application context has not been set
2018-11-17 18:21:18,940 WARN [localhost-startStop-1] [atlassian.confluence.plugin.PluginFrameworkContextListener] contextDestroyed Failed to shut down plugin system during ServletContext shutdown: Spring Application context has not been set
2018-11-17 18:21:18,941 INFO [localhost-startStop-1] [com.atlassian.confluence.lifecycle] contextDestroyed Stopping Confluence
Nov 17, 2018 6:21:19 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [] registered the JDBC driver [org.hsqldb.jdbc.JDBCDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Nov 17, 2018 6:21:19 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Nov 17, 2018 6:21:19 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [Abandoned connection cleanup thread] but has failed to stop it. This is very likely to create a memory leak.
Nov 17, 2018 6:21:19 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8090"]
Nov 17, 2018 6:21:19 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8090"]

Hi dianel,

 

               My issue i have turned off backup plans(daily weekly monthly)

 

"Otherwise you should be alright to start Confluence back up."

 

Thanks,

 

Kannan

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