JIRA fails to start, no logs

[Oliver Lade]

I've installed the standalone JIRA (5.0.1) on a Solaris 10 machine from the archive. Being a bit of a noob, I fiddled around with the startup and shutdown scripts, and it took a while before I could actually see it in the browser (incorrect URL may not have helped...).

In any case, it worked eventually, and I took a couple of steps through the setup wizard. It was unstable though, and the server was prone to crash with some kind of Java error (though I could confirm the MySQL DB configuration was correct). After a couple of shutdowns and startups (often not working if I didn't kill the Java process(es)), I couldn't get it working again, and gave up.

Today I deleted all the JIRA files (/opt/atlassian/jira/ and JIRA_HOME = /var/atlassian/jira/), not knowing a better way to 'uninstall', and even rebooted the machine (in true Windows user fashion - did I mention I'm still trying to figure all this out?). I re-extracted the install files to the same directory with the same JIRA_HOME set, and tried the jira-start.sh script. I receive the message:

****************
JIRA starting...
****************

but nothing after that (presumably something else crashed somewhere). I checked the other logs, but they were empty too. I checked /var/atlassian/jira/ and the whole directory was empty. Running shutdown.sh hangs indefinitely at the end, and running startup.sh says the Tomcat server is already running (abort).

I'm sure that I've done something horribly wrong, but I don't know enough to work out what it is. Can anyone give me some advice about what to remove/reinstall to try to get JIRA working? Is there a way to cleanly remove JIRA, including any Tomcat processes and left over Java things?

[Radu Dumitriu · Accepted solution]

On a unix system, this usually works

A) To kill tomcat without caring too much:

kill - 9 `ps -adef | grep java | grep jira | awk '{ print $2; }'`

#well, take care of the greps above !

rm -rf <JIRA_HOME>/.jira-home.lock

B) To uninstall:

rm -rf <JIRA_HOME>

rm -rf <JIRA_BIN_HOME>

(other files, as for instance your init.d files you used to start/stop Jira)

C) your q; first things to check:

i) Are you running with a good java version? Jira will not run on JDK 7 and for sure will not work on Open JDK. Oracle JDK 6 only.

ii) Permissions on those directories (and check the user you are launching JIRA with)

iii) Permissions on DB (are you able to create tables using the same credentials ?)

[Oliver Lade]

Hmm, this time it got past that point, though I didn't change anything. However after loading up a few plugins, it crashed the JRE and gave me a hs_err log and core dump. Not sure if that's useful or not.

Also, the logs say "Reading database configuration from /var/atlassian/jira/dbconfig.xml", which doesn't seem to exist. Not sure if that means anything either.

Rebooted for something to do, ran the start script again, and it's stuck at "Initialising the plugin system". Sigh.

[Oliver Lade]

Thanks Radu, that's got me back on track!

• Killing everything off properly is very handy, and seems to work well (although sometimes after running it, JIRA still thinks it's alive; removing the "| grep jira" part solves that, dangerous though it may be).
• Hopefully I don't need to uninstall given that it's almost kind of working again, but good to know that's all it takes.
• I was previously running JDK 7, which is evidently a mistake. I've set up a custom start-jira script which looks something like:

export JAVA_HOME=/opt/jdk/jdk1.6.0_30

export JIRA_HOME=/var/atlassian/jira

/opt/atlassian/jira/bin/start-jira.sh && tail -f /opt/atlassian/jira/logs/catalina.out

The catalina.out log is getting stuck on the plugin system:

2012-03-31 21:59:13,903 main INFO      [atlassian.plugin.manager.DefaultPluginManager] Initialising the plugin system

I've dropped the database and re-created it (empty) to try and flush out any previous configuration problems, but I'm not sure if I need to do something else too? DB permissions are okay (can create tables), and I think permissions should be okay since I'm running as root who has rwx to JIRA_HOME.

I get the feeling it just might work if I can just get the server to start properly. Investigating the plugin thing now, any ideas?

[Oliver Lade]

Okay, so now sometimes it initialises the plugin system, doesn't crash spectacularly, and I get to "INFO: Server startup in 30912 ms", but then it hangs again and the server is still not accessible.

I also noticed a Java process running that respawns after I kill it, and looks like this:

noaccess  7763 21598   3 12:00:23 ?           0:13 /usr/java/bin/java -server -Xmx128m -XX:+UseParallelGC -XX:ParallelGCThreads=4

That could be a problem, since /usr/java/bin/java is version 1.5 - I want to use /opt/jdk/1.6.0_03

Then I try again and it gets stuck on initialising the plugin system again. I really don't understand this.

[Radu Dumitriu]

as root, please run bin/startup.sh (to start) and bin/shutdown.sh (to stop it).

I suspect there is a problem with your perms there; start-jira.sh switches the user AFAIK.

HTH

[Oliver Lade]

Hah, yes, should have tried that. Still doesn't work, but I get exceptions this time. When trying startup.sh I got an error (not this one, but this came the next time):

2012-04-02 21:01:15,687 QuartzWorker-1 ERROR      [org.quartz.simpl.SimpleThreadPool] Error while executing the Runnable:
java.lang.IllegalMonitorStateException
        at java.lang.Object.wait(Native Method)
        at org.quartz.simpl.SimpleThreadPool.getNextRunnable(SimpleThreadPool.java:428)
        at org.quartz.simpl.SimpleThreadPool.access$000(SimpleThreadPool.java:47)
        at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:518)

Then when trying shutdown.sh:

Apr 02, 2012 8:59:37 PM org.apache.catalina.startup.Catalina stopServer
SEVERE: Catalina.stop:
java.net.ConnectException: Connection refused
        at java.net.PlainSocketImpl.socketConnect(Native Method)
        at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
        at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
        at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
        at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:391)
        at java.net.Socket.connect(Socket.java:579)
        at java.net.Socket.connect(Socket.java:528)
        at java.net.Socket.<init>(Socket.java:425)
        at java.net.Socket.<init>(Socket.java:208)
        at org.apache.catalina.startup.Catalina.stopServer(Catalina.java:422)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:601)
        at org.apache.catalina.startup.Bootstrap.stopServer(Bootstrap.java:338)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:416)

[Radu Dumitriu]

The second is normal, the first one it's not. Make sure your booting with JDK 1.6

[Oliver Lade]

During startup I get:

___ Java System Properties _________________
[...]
     java.home                                     : /opt/jdk/instances/jdk1.6.0/jre
[...]
     java.runtime.version                          : 1.6.0_30-b12
     java.specification.name                       : Java Platform API Specification
     java.specification.vendor                     : Sun Microsystems Inc.
     java.specification.version                    : 1.6
     java.util.logging.config.file                 : /opt/atlassian/jira/conf/logging.properties
[...]
     sun.boot.library.path                         : /opt/jdk/instances/jdk1.6.0/jre/lib/i386
[...]

But hang on... i386? I downloaded the i586 (x86) version of Java from here... was that right? What does i386 imply? I get:

$ uname -a
SunOS s440gc 5.10 Generic_142901-03 i86pc i386 i86pc
$ isainfo -kv
64-bit amd64 kernel modules

Additional info:

___ Environment _____________________________

     JIRA Build                                    : 5.0.1#721-sha1:838c4a0b95816e00f959efadbfe32a2139ca3829
     Build Date                                    : Thu Mar 15 00:00:00 EST 2012
     JIRA Installation Type                        : Standalone
     Application Server                            : Apache Tomcat/6.0.32 - Servlet API 2.5
     Java Version                                  : 1.6.0_30 - Sun Microsystems Inc.

Any hints? Did I do something stupid?

[Radu Dumitriu]

Your native stuff is on amd64. If I remember well, there's a special version for solaris amd x64 (but I'm not an expert on Solaris and I may be wrong).

http://www.java.com/en/download/help/solaris_x64_install.xml

[Oliver Lade]

Thank you, I followed those instructions and installed the x64 Java packages. I'm not quite sure how to make them execute in preference to the x86 versions, other than adding -d64 to the list of Java arguments (which I don't know where they are), or overwriting $JAVA_HOME/bin with $JAVA_HOME/bin/amd64. Ideas?

I also installed the Connector/J JDBC driver and put it on the CLASSPATH, because it was mentioned in Supported Platforms. It doesn't seem to do anything though.

At least I now seem to be consistently getting that same error about the QuartzMonitor "IllegalMonitorStateException".

[Jo-Anne MacLeod]

did you remember to set up your jira-home directory (and uncomment out the line).

http://confluence.atlassian.com/x/zYFRCw

[Oliver Lade]

I did, to /var/atlassian/jira. It was (kind of) working before, so I assume this is fine.