Unable to create directory for deployment: [/opt/atlassian/jira/conf/Catalina/localhost with JIRA

[Jasper]

For some reason my Jira stopped working and isn't starting up anymore.

This is the Catalina.out file:

08-May-2019 14:49:26.196 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
08-May-2019 14:49:26.209 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 1404 ms
08-May-2019 14:49:26.221 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
08-May-2019 14:49:26.221 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.32
08-May-2019 14:49:26.235 SEVERE [Catalina-startStop-1] org.apache.catalina.startup.HostConfig.beforeStart Unable to create directory for deployment: [/opt/atlassian/jira/conf/Catalina/localhost]
08-May-2019 14:52:36.352 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.5.32
08-May-2019 14:52:36.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Jun 20 2018 19:50:35 UTC
08-May-2019 14:52:36.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.5.32.0
08-May-2019 14:52:36.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
08-May-2019 14:52:36.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 3.10.0-229.el7.x86_64
08-May-2019 14:52:36.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
08-May-2019 14:52:36.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /opt/atlassian/jira/jre
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_181-b13
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /opt/atlassian/jira
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /opt/atlassian/jira
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms384m
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx1023m
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:InitialCodeCacheSize=32m
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:ReservedCodeCacheSize=512m
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.standalone=JIRA
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dmail.mime.decodeparameters=true
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.locale.providers=COMPAT
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xloggc:/opt/atlassian/jira/logs/atlassian-jira-gc-%t.log
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+UseGCLogFileRotation
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:NumberOfGCLogFiles=5
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:GCLogFileSize=20M
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDetails
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDateStamps
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCTimeStamps
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCCause
08-May-2019 14:52:36.383 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
08-May-2019 14:52:36.383 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/opt/atlassian/jira
08-May-2019 14:52:36.383 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/opt/atlassian/jira
08-May-2019 14:52:36.383 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/opt/atlassian/jira/temp
08-May-2019 14:52:36.383 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]
08-May-2019 14:52:37.105 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
08-May-2019 14:52:37.124 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 2229 ms
08-May-2019 14:52:37.158 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
08-May-2019 14:52:37.158 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.32
08-May-2019 14:52:37.185 SEVERE [Catalina-startStop-1] org.apache.catalina.startup.HostConfig.beforeStart Unable to create directory for deployment: [/opt/atlassian/jira/conf/Catalina/localhost]

 Looks like here is something wrong.. But what and how to debug/fix this?

Other files recently changed in /opt/atlassian/jira/logs:

atlassian-jira-gc-2019-05-08_14-52-33.log.0.current

Java HotSpot(TM) 64-Bit Server VM (25.181-b13) for linux-amd64 JRE (1.8.0_181-b13), built on Jul 7 2018 00:56:38 by "java_re" with gcc 4.3.0 20080428 (Red Hat 4.3.0-8)
Memory: 4k page, physical 5794984k(5344612k free), swap 630780k(630780k free)
CommandLine flags: -XX:GCLogFileSize=20971520 -XX:InitialCodeCacheSize=33554432 -XX:InitialHeapSize=402653184 -XX:MaxHeapSize=1072693248 -XX:NumberOfGCLogFiles=5 -XX:-OmitStackTraceInFastThrow -XX:+PrintGC -XX:+PrintGCCause -XX:+PrintGCDateStamps -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:ReservedCodeCacheSize=536870912 -XX:+UseCompressedClassPointers -XX:+UseCompressedOops -XX:+UseGCLogFileRotation -XX:+UseParallelGC 
2019-05-08T14:52:40.982+0200: 7.871: [GC (Allocation Failure) [PSYoungGen: 98304K->11638K(114688K)] 98304K->11718K(376832K), 0.0206140 secs] [Times: user=0.03 sys=0.01, real=0.01 secs] 

catalina.2019-05-08.log

...
08-May-2019 14:49:25.899 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]
08-May-2019 14:49:26.196 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
08-May-2019 14:49:26.209 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 1404 ms
08-May-2019 14:49:26.221 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
08-May-2019 14:49:26.221 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.32
08-May-2019 14:49:26.235 SEVERE [Catalina-startStop-1] org.apache.catalina.startup.HostConfig.beforeStart Unable to create directory for deployment: [/opt/atlassian/jira/conf/Catalina/localhost]
08-May-2019 14:52:36.352 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.5.32
08-May-2019 14:52:36.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Jun 20 2018 19:50:35 UTC
08-May-2019 14:52:36.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.5.32.0
08-May-2019 14:52:36.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
08-May-2019 14:52:36.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 3.10.0-229.el7.x86_64
08-May-2019 14:52:36.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
08-May-2019 14:52:36.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /opt/atlassian/jira/jre
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_181-b13
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /opt/atlassian/jira
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /opt/atlassian/jira
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms384m
08-May-2019 14:52:36.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx1023m
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:InitialCodeCacheSize=32m
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:ReservedCodeCacheSize=512m
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.standalone=JIRA
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dmail.mime.decodeparameters=true
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.locale.providers=COMPAT
08-May-2019 14:52:36.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xloggc:/opt/atlassian/jira/logs/atlassian-jira-gc-%t.log
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+UseGCLogFileRotation
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:NumberOfGCLogFiles=5
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:GCLogFileSize=20M
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDetails
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDateStamps
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCTimeStamps
08-May-2019 14:52:36.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCCause
08-May-2019 14:52:36.383 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
08-May-2019 14:52:36.383 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/opt/atlassian/jira
08-May-2019 14:52:36.383 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/opt/atlassian/jira
08-May-2019 14:52:36.383 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/opt/atlassian/jira/temp
08-May-2019 14:52:36.383 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]
08-May-2019 14:52:37.105 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
08-May-2019 14:52:37.124 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 2229 ms
08-May-2019 14:52:37.158 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
08-May-2019 14:52:37.158 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.32
08-May-2019 14:52:37.185 SEVERE [Catalina-startStop-1] org.apache.catalina.startup.HostConfig.beforeStart Unable to create directory for deployment: [/opt/atlassian/jira/conf/Catalina/localhost]

[Nic Brough -Adaptavist-]

The usual culprit here is that you installed it and ran it with a dedicated user (As you should), but on the penultimate restart, you started the system as another user (probably an admin)

That user took ownership of a load of files and directories.  Then, on the last restart, you went back to the dedicated user, who no longer has full access to the files and directories it needs!

Shut it down again, and check all the ownership and access rights.

[Jasper]

How can I check which user took ownership?

[Nic Brough -Adaptavist-]

Go to /opt/atlassian and use ls -l on some of the directories in there.  If my guess is right, you'll find at least two different owners in most of them.  There should be a single owner for each system.

[Jasper]

What if I do a full chmod 777 to all?

[Jasper]

[root@atlassian jira]# ls -l
totaal 240
drwxr-xr-x 18 root root 4096 15 feb 14:36 atlassian-jira
drwxr-xr-x 3 root root 4096 15 feb 14:36 bin
drwxr-xr-x 2 root root 4096 15 feb 14:36 conf
drwxr-xr-x 2 root root 39 15 feb 14:36 external-source
-rw-r--r-- 1 root root 100561 15 feb 14:37 install.reg
drwxr-xr-x 4 root root 122 15 feb 14:35 jre
drwxr-xr-x 2 root root 4096 15 feb 14:36 lib
drwxr-xr-x 2 root root 57344 15 feb 14:36 licenses
drwx------ 2 jira root 12288 8 mei 14:52 logs
-rw-r--r-- 1 root root 1774 9 feb 08:23 NOTICE
-rw-r--r-- 1 root root 5662 9 feb 08:23 README.html
-rw-r--r-- 1 root root 3512 9 feb 08:23 README.txt
drwx------ 2 jira root 4096 8 mei 01:00 temp
drwxr-xr-x 2 root root 58 15 feb 14:36 tomcat-docs
-rwx------ 1 root root 11200 9 feb 08:25 uninstall
drwxr-xr-x 2 root root 6 9 feb 08:25 webapps
drwx------ 3 jira root 40 8 mei 14:52 work

You are correct. But how to fix this? To have all "jira" as the user instead of Root?

[Jasper]

Figured it out to do it all with chown:

[jira@atlassian bin]$ cd /opt/atlassian/jira
[jira@atlassian jira]$ ls -l
total 240
drwxr-xr-x 18 jira jira 4096 Feb 15 14:36 atlassian-jira
drwxr-xr-x 3 jira jira 4096 Feb 15 14:36 bin
drwxr-xr-x 3 jira jira 4096 May 8 18:05 conf
drwxr-xr-x 2 jira jira 39 Feb 15 14:36 external-source
-rw-r--r-- 1 jira jira 100561 Feb 15 14:37 install.reg
drwxr-xr-x 4 jira jira 122 Feb 15 14:35 jre
drwxr-xr-x 2 jira jira 4096 Feb 15 14:36 lib
drwxr-xr-x 2 jira jira 57344 Feb 15 14:36 licenses
drwxrwxrwx 2 jira jira 12288 May 8 18:19 logs
-rw-r--r-- 1 jira jira 1774 Feb 9 08:23 NOTICE
-rw-r--r-- 1 jira jira 5662 Feb 9 08:23 README.html
-rw-r--r-- 1 jira jira 3512 Feb 9 08:23 README.txt
drwx------ 2 jira jira 4096 May 8 01:00 temp
drwxr-xr-x 2 jira jira 58 Feb 15 14:36 tomcat-docs
-rwx------ 1 jira jira 11200 Feb 9 08:25 uninstall
drwxr-xr-x 2 jira jira 6 Feb 9 08:25 webapps
drwx------ 3 jira jira 40 May 8 18:15 work

But still the output is this:

[root@atlassian ~]# sudo su - jira
Laatste aanmelding: wo 8 mei 18:10:39 CEST 2019 op pts/0
[jira@atlassian ~]$ cd /opt/atlassian/jira
[jira@atlassian jira]$ cd bin/
[jira@atlassian bin]$ ./st
start-jira.sh startup.sh stop-jira.sh
[jira@atlassian bin]$ ./start-jira.sh -fg
executing as current user

`sMMMMMMMMMMMMMM+
MMMMMMMMMMMMMM
:sdMMMMMMMMMMM
MMMMMM
`sMMMMMMMMMMMMMM+ MMMMMM
MMMMMMMMMMMMMM +MMMMM
:sMMMMMMMMMMM MMMMM
MMMMMM `UOJ
`sMMMMMMMMMMMMM+ MMMMMM
MMMMMMMMMMMMMM +MMMMM
:sdMMMMMMMMMM MMMMM
MMMMMM `UOJ
MMMMMM
+MMMMM
MMMMM
`UOJ

Atlassian Jira
Version : 8.0.0


If you encounter issues starting or stopping JIRA, please see the Troubleshooting guide at https://docs.atlassian.com/jira/jadm-docs-080/Troubleshooting+installation


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
08-May-2019 18:19:43.588 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.5.32
08-May-2019 18:19:43.589 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Jun 20 2018 19:50:35 UTC
08-May-2019 18:19:43.589 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.5.32.0
08-May-2019 18:19:43.589 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
08-May-2019 18:19:43.589 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 3.10.0-229.el7.x86_64
08-May-2019 18:19:43.590 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
08-May-2019 18:19:43.590 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /opt/atlassian/jira/jre
08-May-2019 18:19:43.590 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_181-b13
08-May-2019 18:19:43.590 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
08-May-2019 18:19:43.590 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /opt/atlassian/jira
08-May-2019 18:19:43.590 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /opt/atlassian/jira
08-May-2019 18:19:43.590 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties
08-May-2019 18:19:43.590 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
08-May-2019 18:19:43.591 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms384m
08-May-2019 18:19:43.591 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx1023m
08-May-2019 18:19:43.591 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:InitialCodeCacheSize=32m
08-May-2019 18:19:43.591 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:ReservedCodeCacheSize=512m
08-May-2019 18:19:43.591 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
08-May-2019 18:19:43.591 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.standalone=JIRA
08-May-2019 18:19:43.591 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true
08-May-2019 18:19:43.591 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dmail.mime.decodeparameters=true
08-May-2019 18:19:43.591 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
08-May-2019 18:19:43.592 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow
08-May-2019 18:19:43.592 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.locale.providers=COMPAT
08-May-2019 18:19:43.592 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.plugins.startup.options=-fg
08-May-2019 18:19:43.592 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
08-May-2019 18:19:43.592 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
08-May-2019 18:19:43.592 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
08-May-2019 18:19:43.592 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xloggc:/opt/atlassian/jira/logs/atlassian-jira-gc-%t.log
08-May-2019 18:19:43.592 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+UseGCLogFileRotation
08-May-2019 18:19:43.592 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:NumberOfGCLogFiles=5
08-May-2019 18:19:43.592 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:GCLogFileSize=20M
08-May-2019 18:19:43.592 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDetails
08-May-2019 18:19:43.593 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDateStamps
08-May-2019 18:19:43.593 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCTimeStamps
08-May-2019 18:19:43.594 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCCause
08-May-2019 18:19:43.594 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
08-May-2019 18:19:43.594 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/opt/atlassian/jira
08-May-2019 18:19:43.594 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/opt/atlassian/jira
08-May-2019 18:19:43.594 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/opt/atlassian/jira/temp
08-May-2019 18:19:43.594 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]
08-May-2019 18:19:43.897 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
08-May-2019 18:19:43.906 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 2170 ms
08-May-2019 18:19:43.943 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
08-May-2019 18:19:43.943 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.32
Killed

[Nic Brough -Adaptavist-]

Who is the process running as now?  A quick "ps -ef | grep -i jira" run in as it starts up, should show you the owner of the process.

[Jasper]

[root@atlassian ~]# ps -ef | grep -i jira
root 2607 1 31 18:55 ? 00:00:05 /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 -Xms384m -Xmx1023m -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 -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
root 2801 2531 0 18:55 pts/0 00:00:00 grep --color=auto -i jira

[Jasper]

[jira@atlassian ~]$ ps -ef | grep -i jira
root 4230 4164 0 19:05 pts/0 00:00:00 sudo su - jira
root 4231 4230 0 19:05 pts/0 00:00:00 su - jira
jira 4232 4231 0 19:05 pts/0 00:00:00 -bash
jira 4315 4232 0 19:05 pts/0 00:00:00 ps -ef
jira 4316 4232 0 19:05 pts/0 00:00:00 grep --color=auto -i jira
[jira@atlassian ~]$ exit
logout
[root@atlassian ~]# ps -ef | grep -i jira
root 4341 4164 0 19:06 pts/0 00:00:00 grep --color=auto -i jira

[Nic Brough -Adaptavist-]

Ok, that's the same problem - you've managed to start Jira as root, which clobbers half the files.  You'll need to stop it, chown everything back again, then restart it as the jira user.

If you're logged in as root, you should be able to use either systemctl or /etc/init.d scripts to start it as the right user.

[Jasper]

What steps to do? I can't correctly stop them without getting mentions about tomcat having trouble with Catalina etc.

Can you provide me with some steps to solve it/?

[Nic Brough -Adaptavist-]

There is not a lot more I can tell you - stop the service, ideally cleanly, but make sure it is completely stopped.  Correct the file ownerships, and restart it as the right user, using the start-up system you've got (systemd's systemctl or the older but perfectly functional /etc/init.d system)

[Jasper]

Is there help to stop all Jira services that are running that moment? I though I did, but it didn't work. Cause I did this afterwards:

chown -R jira:jira /opt/atlassian/jira

And then went to /etc/init.d and ran ./jira start

[Jasper]

Will it work if I upgrade Jira to latest version?

[Nic Brough -Adaptavist-]

The upgrade process should correct the ownership of files, but it won't change whatever it is that is running the process as the wrong user.

[Jasper]

@Nic Brough -Adaptavist- so how to kill all processes and be sure they are 

[Nic Brough -Adaptavist-]

ps -ef shows you the details of all running processes, and kill -9 stops a process dead, no matter what.

[jy]

mine had this error due to a keystore issue, when i tried to change to a new keystore this error appear. When I reverted back, the application could startup normally. Weird that the catalina.out logs didn't say its a keystore issue, and say its can't create this directory, memory leak