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Hi, I had a problem with confluence and Jira. I decided to start again. I went into root via FTP and erased all of the atlassian folders. So then I ran ./atlassian-jira-software-7.1.6-jira-7.1.6-x64.bin via putty.


The port is open and not fire walled. Any ideas? My server meets the requirements because I had both Jira and Confluence installed before. Please help!


[root@server ~]# sudo /etc/init.d/jira start

To run JIRA in the foreground, start the server with start-jira.sh -fg
executing using dedicated user: jira1
.... .NMMMD. ...
.8MMM. $MMN,..~MMMO.
.?MMM. .MMM?.


Atlassian JIRA
Version : 7.1.6

If you encounter issues starting or stopping JIRA, please see the Troubleshootin g guide at http://confluence.atlassian.com/display/JIRA/Installation+Troubleshoo ting+Guide

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
touch: cannot touch `/opt/atlassian/jira/logs/catalina.out': Permission denied
/opt/atlassian/jira/bin/catalina.sh: line 404: /opt/atlassian/jira/logs/catalina .out: Permission denied
[root@server ~]# touch: cannot touch `/opt/atlassian/jira/logs/catalina.out': Pe rmission denied
> /opt/atlassian/jira/bin/catalina.sh: line 404: /opt/atlassian/jira/logs/catali natouch: cannot touch `/opt/atlassian/jira/logs/catalina.out': Permission denied
> /opt/atlassian/jira/bin/catalina.sh: line 404: /opt/atlassian/jira/logs/catali natouch: cannot touch `/opt/atlassian/jira/logs/catalina.out': Permission denied
-bash: command substitution: line 1: unexpected EOF while looking for matching ` ''
-bash: command substitution: line 3: syntax error: unexpected end of file
-bash: touch:: command not found
[root@server ~]# /opt/atlassian/jira/bin/catalina.sh: line 404: /opt/atlassian/j ira/logs/catalina^C

1 answer

0 vote

It looks like you've installed it incorrectly - the ownership of the installation is messed up from all those "permission denied" errors.  When you deleted everything, are you sure you got everything - both JIRA and Confluence's installation AND home directories, and the stuff the installer adds to /etc?


I fixed the permissions, restarted the server but the url still will not load. I get this now:

[root@server ~]# sudo /etc/init.d/jira start

To run JIRA in the foreground, start the server with start-jira.sh -fg
executing using dedicated user: jira1
.... .NMMMD. ...
.8MMM. $MMN,..~MMMO.
.?MMM. .MMM?.


Atlassian JIRA
Version : 7.1.6

If you encounter issues starting or stopping JIRA, please see the Troubleshooting guide at http://confluence.atlassian.com/display/JIRA/Installation+Troubleshooting+Guide

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
Tomcat started.

Ok, great, that's the basics fixed - Tomcat is now starting, so you can move on to the JIRA log - have a look in <jira-home>/logs/atlassian-jira.log

Here is the log:

2016-05-12 15:33:56,158 JIRA-Bootstrap INFO      [c.a.jira.startup.JiraStartupLogger]
    JIRA starting...
2016-05-12 15:33:56,463 localhost-startStop-1 INFO      [c.a.jira.startup.JiraHomeStartupCheck] The jira.home directory '/var/atlassian/application-data/jira' is validated and locked for exclusive use by this instance.
2016-05-12 15:33:56,571 JIRA-Bootstrap INFO      [c.a.jira.startup.JiraStartupLogger]
    ___ Environment _____________________________
         JIRA Build                                    : 7.1.6#71010-sha1:428b2b30f0d03f9b8f93ae6d2da3161a73521453
         Build Date                                    : Thu Apr 28 00:00:00 BST 2016
         JIRA Installation Type                        : Standalone
         Application Server                            : Apache Tomcat/8.0.17 - Servlet API 3.1
         Java Version                                  : 1.8.0_74 - Oracle Corporation
         Current Working Directory                     : /opt/atlassian/jira/bin
         Maximum Allowable Memory                      : 683MB
         Total Memory                                  : 496MB
         Free Memory                                   : 375MB
         Used Memory                                   : 121MB
         Memory Pool: Code Cache                       : Code Cache: init = 2555904(2496K) used = 8957504(8747K) committed = 9043968(8832K) max = 251658240(245760K)
         Memory Pool: Metaspace                        : Metaspace: init = 0(0K) used = 20230320(19756K) committed = 20840448(20352K) max = -1(-1K)
         Memory Pool: Compressed Class Space           : Compressed Class Space: init = 0(0K) used = 2319416(2265K) committed = 2490368(2432K) max = 1073741824(1048576K)
         Memory Pool: PS Eden Space                    : PS Eden Space: init = 100663296(98304K) used = 65032328(63508K) committed = 234881024(229376K) max = 234881024(229376K)
         Memory Pool: PS Survivor Space                : PS Survivor Space: init = 16777216(16384K) used = 16769904(16376K) committed = 16777216(16384K) max = 16777216(16384K)
         Memory Pool: PS Old Gen                       : PS Old Gen: init = 268435456(262144K) used = 46078120(44998K) committed = 268435456(262144K) max = 536870912(524288K)
         JVM Input Arguments                           : -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms384m -Xmx768m -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:+PrintGCDateStamps -XX:-OmitStackTraceInFastThrow -Djava.endorsed.dirs=/opt/atlassian/jira/endorsed -Dcatalina.base=/opt/atlassian/jira -Dcatalina.home=/opt/atlassian/jira -Djava.io.tmpdir=/opt/atlassian/jira/temp
         Java Compatibility Information                : JIRA version = 7.1.6, Java Version = 1.8.0_74
    ___ Java System Properties _________________
         atlassian.standalone                          : JIRA
         awt.toolkit                                   : sun.awt.X11.XToolkit
         catalina.base                                 : /opt/atlassian/jira
         catalina.home                                 : /opt/atlassian/jira
         catalina.useNaming                            : true
         common.loader                                 : "${catalina.base}/lib",
         file.encoding                                 : UTF-8
         file.encoding.pkg                             : sun.io
         java.awt.graphicsenv                          : sun.awt.X11GraphicsEnvironment
         java.awt.headless                             : true
         java.awt.printerjob                           : sun.print.PSPrinterJob
         java.class.version                            : 52.0
         java.home                                     : /opt/atlassian/jira/jre
         java.io.tmpdir                                : /opt/atlassian/jira/temp
         java.naming.factory.initial                   : org.apache.naming.java.javaURLContextFactory
         java.naming.factory.url.pkgs                  : org.apache.naming
         java.runtime.name                             : Java(TM) SE Runtime Environment
         java.runtime.version                          : 1.8.0_74-b02
         java.specification.name                       : Java Platform API Specification
         java.specification.vendor                     : Oracle Corporation
         java.specification.version                    : 1.8
         java.util.logging.config.file                 : /opt/atlassian/jira/conf/logging.properties
         java.util.logging.manager                     : org.apache.juli.ClassLoaderLogManager
         java.vendor                                   : Oracle Corporation
         java.vendor.url                               : http://java.oracle.com/
         java.vendor.url.bug                           : http://bugreport.sun.com/bugreport/
         java.version                                  : 1.8.0_74
         java.vm.info                                  : mixed mode
         java.vm.name                                  : Java HotSpot(TM) 64-Bit Server VM
         java.vm.specification.name                    : Java Virtual Machine Specification
         java.vm.specification.vendor                  : Oracle Corporation
         java.vm.specification.version                 : 1.8
         java.vm.vendor                                : Oracle Corporation
         java.vm.version                               : 25.74-b02
         mail.mime.decodeparameters                    : true
         org.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER : true
         org.dom4j.factory                             : com.atlassian.core.xml.InterningDocumentFactory
         os.arch                                       : amd64
         os.name                                       : Linux
         os.version                                    : 2.6.32-573.26.1.el6.x86_64
         package.access                                : sun.,
         package.definition                            : sun.,
         server.loader                                 :
         shared.loader                                 :
         sun.arch.data.model                           : 64
         sun.boot.library.path                         : /opt/atlassian/jira/jre/lib/amd64
         sun.cpu.endian                                : little
         sun.cpu.isalist                               :
         sun.io.unicode.encoding                       : UnicodeLittle
         sun.java.command                              : org.apache.catalina.startup.Bootstrap start
         sun.java.launcher                             : SUN_STANDARD
         sun.jnu.encoding                              : UTF-8
         sun.management.compiler                       : HotSpot 64-Bit Tiered Compilers
         sun.os.patch.level                            : unknown
         tomcat.util.buf.StringCache.byte.enabled      : true
         tomcat.util.scan.StandardJarScanFilter.jarsToScan : log4j-core*.jar,log4j-taglib*.jar
         tomcat.util.scan.StandardJarScanFilter.jarsToSkip : bootstrap.jar,
         user.country                                  : GB
         user.dir                                      : /opt/atlassian/jira/bin
         user.home                                     : /home/jira1
         user.language                                 : en
         user.name                                     : jira1
         user.timezone                                 : Europe/London
2016-05-12 15:33:57,945 JIRA-Bootstrap INFO      [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/application-data/jira/dbconfig.xml
2016-05-12 15:33:58,216 JIRA-Bootstrap INFO      [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/application-data/jira/dbconfig.xml
2016-05-12 15:33:58,783 JIRA-Bootstrap INFO      [c.a.jira.startup.JiraStartupLogger]
    ___ Starting the JIRA Plugin System _________________
2016-05-12 15:33:58,859 JIRA-Bootstrap INFO      [c.a.plugin.manager.DefaultPluginManager] Plugin system earlyStartup begun
2016-05-12 15:34:08,337 JIRA-Bootstrap INFO      [c.a.plugin.loaders.ScanningPluginLoader] No plugins found to be deployed
2016-05-12 15:34:09,722 ThreadPoolAsyncTaskExecutor::Thread 5 WARN      [c.a.p.s.scanner.util.ProductFilterUtil] Couldn't detect product, will use ProductFilter.ALL
2016-05-12 15:34:09,778 JIRA-Bootstrap INFO      [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (13): [tac.jira core.languages.es_ES, com.atlassian.plugins.less-transformer-plugin, tac.jira core.languages.de_DE, tac.jira core.languages.fr_FR, com.atlassian.auiplugin, com.atlassian.plugins.issue-status-plugin, com.atlassian.soy.soy-template-plugin, tac.jira core.languages.ja_JP, com.atlassian.jira.jira-languages.en_US, com.atlassian.plugin.jslibs, com.atlassian.jira.jira-less-integration, com.atlassian.jira.jira-languages.en_UK, com.atlassian.plugins.jquery], 60 seconds remaining
2016-05-12 15:34:11,568 JIRA-Bootstrap INFO      [c.a.plugin.manager.DefaultPluginManager] Plugin system earlyStartup ended
2016-05-12 15:34:12,542 JIRA-Bootstrap INFO      [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/application-data/jira/dbconfig.xml
2016-05-12 15:34:12,592 JIRA-Bootstrap INFO      [c.a.j.instrumentation.external.DatabaseExternalGauges] Installing DBCP monitoring instruments: DatabaseExternalGauges.JiraDbcpInstruments[instruments=[DBCP_MAX, DBCP_ACTIVE, DBCP_IDLE],objectName=com.atlassian.jira:name=BasicDataSource]
2016-05-12 15:34:12,757 JIRA-Bootstrap INFO      [c.a.jira.startup.JiraStartupLogger] Running JIRA startup checks.
2016-05-12 15:34:12,775 JIRA-Bootstrap INFO      [c.a.jira.startup.JiraStartupLogger] JIRA pre-database startup checks completed successfully.
2016-05-12 15:34:13,130 JIRA-Bootstrap INFO      [c.a.j.config.database.DatabaseConfigurationManagerImpl] The database is not yet configured. Enqueuing Database Checklist Launcher on post-database-configured-but-pre-database-activated queue
2016-05-12 15:34:13,131 JIRA-Bootstrap INFO      [c.a.j.config.database.DatabaseConfigurationManagerImpl] The database is not yet configured. Enqueuing Post database-configuration launchers on post-database-activated queue
2016-05-12 15:34:13,515 JIRA-Bootstrap INFO      [c.a.jira.startup.LauncherContextListener] Memory Usage:
      Heap memory     :  Used:  149 MiB.  Committed:  459 MiB.  Max:  735 MiB
      Non-heap memory :  Used:   64 MiB.  Committed:   66 MiB.  Max: 1264 MiB
      TOTAL           :  Used:  212 MiB.  Committed:  525 MiB.  Max: 1999 MiB


Any suggestions? I am desperate!!

Not sure if it's relevant, but there is no dbconfig.xml file. I created one but it makes no difference.

Also, If I do a clean install, what folders do I erase? I need to know all of the folders. This will be a last resort if it's not easy to fix. I need to get it working this weekend.


Thank you.


When you get to a "database is not configured" line, that means it's up and running and waiting for you to tell it what to configure for the database.  Connect to it with a browser.  Note that you'll need to work out where it's running (given the defaults, it'll be on <server>:8080)

How do I do this? Yes it's via 8080 but if you can run me through this I'd really appropriate it. I was hoping to set it up via the browser. 

You should be able to visit localhost:8080 on the server to see it.  If the server has no browser functions, you'll need to visit <server>:8080 - if that doesn't respond, then what is the error message or symptom? 

No error message,it just doesn't load and eventually times out. 

Hmm.  That suggests that you are landing on a recognised url with no application behind it.  The next thing to look at is where you think the application should serve up data, and what the Tomcat says is happening.


How exactly do I do that? thank you.

Sorry, I missed the "times out" part.  That means Tomcat is waiting for the application to generate data, and it never does.  That's where you need to look again at atlassian-jira.log - if it's a timeout, you'll find a load of error messages in it.

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