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[Dianna Newman]

Please add any details that might help us help you.

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.

http://pluranet.com:8080/

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?.

OMMMMZ. .,NMMMN~
.IMMMMMM. .NMMMN. .MMMMMN,
,MMMMMM$..3MD..ZMMMMMM.
=NMMMMMM,. .,MMMMMMD.
.MMMMMMMM8MMMMMMM,
.ONMMMMMMMMMMZ.
,NMMMMMMM8.
.:,.$MMMMMMM
.IMMMM..NMMMMMD.
.8MMMMM: :NMMMMN.
.MMMMMM. .MMMMM~.
.MMMMMN .MMMMM?.

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

[Nic Brough -Adaptavist-]

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?

[Dianna Newman]

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?.

OMMMMZ. .,NMMMN~
.IMMMMMM. .NMMMN. .MMMMMN,
,MMMMMM$..3MD..ZMMMMMM.
=NMMMMMM,. .,MMMMMMD.
.MMMMMMMM8MMMMMMM,
.ONMMMMMMMMMMZ.
,NMMMMMMM8.
.:,.$MMMMMMM
.IMMMM..NMMMMMD.
.8MMMMM: :NMMMMN.
.MMMMMM. .MMMMM~.
.MMMMMN .MMMMM?.

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.

[Nic Brough -Adaptavist-]

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

[Dianna Newman]

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                                 : "${catalina.base}/lib",
                                                         "${catalina.base}/lib/*.jar",
                                                         "${catalina.home}/lib",
                                                         "${catalina.home}/lib/*.jar"
         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.,
                                                         org.apache.catalina.,
                                                         org.apache.coyote.,
                                                         org.apache.jasper.,
                                                         org.apache.tomcat.
         package.definition                            : sun.,
                                                         java.,
                                                         org.apache.catalina.,
                                                         org.apache.coyote.,
                                                         org.apache.jasper.,
                                                         org.apache.naming.,
                                                         org.apache.tomcat.
         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,
                                                         commons-daemon.jar,
                                                         tomcat-juli.jar,
                                                         annotations-api.jar,
                                                         el-api.jar,
                                                         jsp-api.jar,
                                                         servlet-api.jar,
                                                         websocket-api.jar,
                                                         catalina.jar,
                                                         catalina-ant.jar,
                                                         catalina-ha.jar,
                                                         catalina-storeconfig.jar,
                                                         catalina-tribes.jar,
                                                         jasper.jar,
                                                         jasper-el.jar,
                                                         ecj-*.jar,
                                                         tomcat-api.jar,
                                                         tomcat-util.jar,
                                                         tomcat-util-scan.jar,
                                                         tomcat-coyote.jar,
                                                         tomcat-dbcp.jar,
                                                         tomcat-jni.jar,
                                                         tomcat-spdy.jar,
                                                         tomcat-websocket.jar,
                                                         tomcat-i18n-en.jar,
                                                         tomcat-i18n-es.jar,
                                                         tomcat-i18n-fr.jar,
                                                         tomcat-i18n-ja.jar,
                                                         tomcat-juli-adapters.jar,
                                                         catalina-jmx-remote.jar,
                                                         catalina-ws.jar,
                                                         tomcat-jdbc.jar,
                                                         tools.jar,
                                                         commons-beanutils*.jar,
                                                         commons-codec*.jar,
                                                         commons-collections*.jar,
                                                         commons-dbcp*.jar,
                                                         commons-digester*.jar,
                                                         commons-fileupload*.jar,
                                                         commons-httpclient*.jar,
                                                         commons-io*.jar,
                                                         commons-lang*.jar,
                                                         commons-logging*.jar,
                                                         commons-math*.jar,
                                                         commons-pool*.jar,
                                                         jstl.jar,
                                                         geronimo-spec-jaxrpc*.jar,
                                                         wsdl4j*.jar,
                                                         ant.jar,
                                                         ant-junit*.jar,
                                                         aspectj*.jar,
                                                         jmx.jar,
                                                         h2*.jar,
                                                         hibernate*.jar,
                                                         httpclient*.jar,
                                                         jmx-tools.jar,
                                                         jta*.jar,
                                                         log4j*.jar,
                                                         mail*.jar,
                                                         slf4j*.jar,
                                                         xercesImpl.jar,
                                                         xmlParserAPIs.jar,
                                                         xml-apis.jar,
                                                         junit.jar,
                                                         junit-*.jar,
                                                         ant-launcher.jar,
                                                         cobertura-*.jar,
                                                         asm-*.jar,
                                                         dom4j-*.jar,
                                                         icu4j-*.jar,
                                                         jaxen-*.jar,
                                                         jdom-*.jar,
                                                         jetty-*.jar,
                                                         oro-*.jar,
                                                         servlet-api-*.jar,
                                                         tagsoup-*.jar,
                                                         xmlParserAPIs-*.jar,
                                                         xom-*.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.

[Nic Brough -Adaptavist-]

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)

[Dianna Newman]

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. 

[Nic Brough -Adaptavist-]

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? 

[Dianna Newman]

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

[Nic Brough -Adaptavist-]

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.

[Dianna Newman]

How exactly do I do that? thank you.

[Nic Brough -Adaptavist-]

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.