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Some linux distributions (notably Debian and Ubuntu) come with a free version of Java called GIJ (from the GCJ project) pre-installed:

jturner:~$ java -version
java version "1.4.2"
gij (GNU libgcj) version 4.1.2 (Ubuntu 4.1.2-0ubuntu5)

Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO

Unfortunately GCJ is incomplete, and unable to run Atlassian Java applications without problems.

The solution is to install a supported version of Java. (tick) Visit the Java download page on the Oracle web site to download a supported version of Java for your Linux distribution. Installation instructions are provided on this web site.

After doing this, make sure the correct version of Java is in use by running java -version:

jturner:~$ java -version
java version "1.6.0"
Java(TM) SE Runtime Environment (build 1.6.0-b105)
Java HotSpot(TM) Server VM (build 1.6.0-b105, mixed mode)

If the GCJ Java is still being used, you will need to explicitly set Linux's default Java platform to a JIRA-supported (e.g. Oracle's) Java platform as the default:

jturner:~$ sudo update-alternatives --config java

There are 2 alternatives which provide `java'.

  Selection    Alternative
*         1    /usr/bin/gij-wrapper-4.1
 +        2    /usr/lib/jvm/java-6-sun/jre/bin/java

Press enter to keep the default[*], or type selection number: 2
Using `/usr/lib/jvm/java-6-sun/jre/bin/java' to provide `java'.


Some programs like Tomcat (bundled with most Atlassian products) need a JAVA_HOME variable set, so they know where Java is installed. This can be set system-wide in /etc/profile:

jturner:~$ sudo su -
root:~# cat >> /etc/profile
export JAVA_HOME

The variable will be set for new terminals:

jturner:~$ echo $JAVA_HOME
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  1. Hi Jeff, Thanks for the tip on configuring Java w/Umbuntu Linux. Re: the latest release of Debian Linux (v5.03 Lenny), the sun-java6-jdk package is not available as an apt-get .deb package (not yet released). I found this information re: available JAVA packages for Debian v5.x:

    Any idea which alternate JVM/JRE would support JIRA v4? Has Atlassian verified JIRA v4 operation with FreeBSD (Unix) or another Linux distribution?

    Many thanks for you work.

    1. The problem with freeBSD is that in order get Java onto it, they've needed to build it against that platform, ie taken the source of the SUN JRE and compiled in natively on BSD. The difference is that for Linux, SUN itself produces the binaries, which is why there are issues in freeBSD support. FYI Ive been using Ubuntu for a couple of years with Jira 3.x and and am testing with Jira4, I foresee no issues.

      1. Anonymous

        Andy, thanks for that info. I've got free BSD v7.2 installed on my Macbook Pro via a VM instance. As I just got my Debian VM instance running java-6-sun JRE, I am going to go forward with testing JIRA v4 on Debian. Good to know that JIRA 3.x runs on Ubuntu. When I installed Ubuntu Desktop v9.0.4, it was good to find that Sun Java 6 was already installed rather than the GNU GJC  version.

        P.S. Some more good info re: JIRA 4.x on Linux here:

  2. Thanks Jeff for this reference.

    James, I think what you need is just edit your repositories on /etc/apt/sources.list and add non-free at the end of each repository.  By default, Debian setup only has main repository defined.

    After changes, you should be able to install sun-java6-jdk as explained here.


    1. Manuel,

      Yes, after adding the non-free reference to my sources list, I was able to download Sun Java 6. Thanks for the tip.

      1. Anonymous

        Hi James,

        Can you provide me your source list?

    2. The specific lines in the /etc/apt/sources.list file are:

    3. Anonymous

      the prob with me i m installing java on my ubuntu ultimate...aftre 93% installation it says unable to fetch some archives

      what should i do?

    4. Anonymous

      Then apt-get update!

  3. Hi.. can you tell me where I can download java sun for ubuntu 9.10?
    I am a new user linux

  4. Two problems:

    1. sun-java6-jdk is not available on Ubuntu 10.10. What alternate package would you recommend? There's a few.
    2. Are you sure we need the java development kit (jdk)? JDK = if you're developing a product. Java runtime engine (JRE) is what you use just to run software.

    Anything wrong with Ubuntu's default-jre package?

    1. Hello Aren,

      No worries. You can get the sun-java6-jdk on Ubuntu LTS 10.04. I am currently participating in the Atlassian Dragons Challenge and using Ubuntu 10.04 with Sun JDK

      1) First, click on System Menu > Administration > Software Sources

      2) Under the ,Other Software Tab, check Ubuntu Partner Repository

      3) Click Reload and issue the following command to get the JDK through Synaptic Package Manager or APT-get

      4) sudo apt-get install sun-java6-jdk and Voila :)

      Good Luck!


  5. Anonymous


    I've some problems installing JIRA 4.4 on Ubuntu 10.4. When I run command:

    sudo ./atlassian-jira-4.4-x64.bin

    then I've got error message:

    Unpacking JRE ...
    Starting Installer ...
    /home/krzysztofku/Downloads/atlassian-jira-4.4-x64.bin.2688.dir/jre/bin/java: 1: Syntax error: "(" unexpected

    If I change shell from sh (in Ubuntu currently sh i dash) to bash and I run:

    sudo ./atlassian-jira-4.4-x64.bin

    I've got other error message:

    Unpacking JRE ...
    Starting Installer ...
    ./atlassian-jira-4.4-x64.bin: line 466: /home/krzysztofku/Downloads/atlassian-jira-4.4-x64.bin.2752.dir/jre/bin/java: cannot execute binary file

    I don't know what I can do next.

    Sorry for my poor english.

    Best regards

    1. Anonymous

      1. Anonymous

  6. Anonymous

    Hello, I followed these instructions EXACTLY, and get as far as java -version, successfully. However, thats as far as I get. When I try to check the version number, I get, "Cannot execute binary file". I am running a 32 bit machine, and I was sure to download the 32 bit version. Any ideas?


    I am running ubuntu 10.04

    1. I actually just tried exactly this, the jdk-6u32-linux-i586.bin file appears valid but the binaries are not executable.  The option to try next is an earlier java release, unfortuantely, Oracle force a login to download, and I can vouch that password reminders are not instant (tongue)

  7. Anonymous

    hey im trying to get sun java on linux deb. you think you can help?


  8. Anonymous

    ahhh this has been such a headache for so long and you tutorial was the remedy I needed. Cannot thank you enough!


  9. Advice to install a supported JRE would seem to conflict with documentation "How to Use System JRE Instead of Embedded JRE" which states that the JIRA installer implements an embedded JRE. Please clarify

  10. Hi all. I installed atlassian-jira-6.2.7-x64 on a debian 7.5 server. everything went fine wit instalation but when I try to access IP:8080,nothing happens. I alredy cecked and port 8080 is open as http proxy. anyone knows how I can reach JIRA?

    BTW, I have apache installed on the server - might that be the problem?

    Thanks in advance.



    I am not sure that JIRA 6.2.7 would be the best one for my debian 7.5 server (but it was the one I got from