12 Sep 2011

Jira on the Synology NAS with HTTPS (Dragon Quest)


Atlassian Synology Dragon Quest Stage 1+2

In this article I am taking the Atlassian Dragon Quest and implement the full JIRA Suite:

On a vanilla Synology DS1511+ NAS with 3Gb memory.

Intended audience
Audience is every DS1010+ & DS1511+ (future) Owner who likes to do development on his NAS. I'm not expecting it to handle 100's of developers, however for the 1-10 users my guess is: it's a fine setup.

The DS1511+ & DS1010+ are Intel Atom based systems, fully x86-64 compatible running a stripped down version of linux x64. The default configuration comes with 1Gb and is official expandable to 3Gb. However also working configurations of 5Gb have been reported.

For an install with only Jira, the 1Gb is sufficient and it even doesn't need to be bootstrapped since Jira comes with its own JRE & Tomcat + we can use the internal MySQL database.

For the complete dragon Quest, I've upgraded the DS1511+ with an additional 2Gb from Kingston SODIMM DDR2-800 2GB CL5.0 (KVR800D2S5/2G). The Original memory module is €82, The Kingston is €21 so take your pick ;-).

I've tried to run Jira + FishEye with 1Gb and it just is to tight. Perhaps if you tweak it's memory usages it might work. However better spend 21 buck on a memory upgrade and save your self the day(s) of trouble.

Let's step back and analyse our playing field and potential pitfalls

The Synology OS (DSM 3.2) comes with two internal databases: MySQL and Postgres. Both are used internally and are configured for light internal use only. They are trimmed down in memory usages and not configured for heavy query material.

=> The previous proof-of-concept install with the internal MySQL  I learned the internal MySQL db is hard to tweak and "if" I tweaked it, the tweaks are reversed after each upgrade of the DSM.
For the sake of Freedom: We will use a dedicated stand alone install of Postgresql.

Preparation of the Synology Dragon's Lair

First we are going to prepare the vanilla Synology for some serious work. Enable SSH and login in as root on your NAS which has the same password as your admin from the webinterface.

Login as admin on the webinterface:  ControlPanel->Teminal -> [X] Enable SSH service

We are now downloading the bootstrap, please make sure you have the latest version.
ssh root@_your_nas_ip
wget http://ipkg.nslu2-linux.org/feeds/optware/syno-i686/cross/stable/syno-i686-bootstrap_1.2-7_i686.xsh

chmod 700 syno-i686-bootstrap_1.2-7_i686.xsh
ipkg update
ipkg install bash
ipkg install coreutils
ipkg install man

Now make your choice on your SCM ( cvs, svn, grit ... ) I'll pick SVN

ipkg install svn
For setup svn on the NAS look here:

Congratulations! Your preparation is finished! We can now start with the Dragon's Quest!

Dragons Stage 1 - Install JIRA

Check your self in on twitter for the Quest on the Dragon's Quest Page HERE.
We will follow the instructions step by step and adjust it for the Synology.

Step 1. Install Java

Read the instructions of step 1
On the Synology we do not install the java binary blindly since the /root partition is only limited in size, we are installing it on the /opt directory with a symbolic link to /opt/java and set the JAVA_HOME to the /opt/java
On September 11th 2011 Java 7 did not work on the Synology DSM 3.2, Java 1.6.27 does!
Unpack it in /opt and make a symbolic link to java.

ln -s /opt/jdk1.6.0_27 /opt/java

Add java to the path and set JAVA_HOME in the /etc/profile file

vi /etc/profile
export JAVA_HOME

Step 1/Stage 1 is complete now!

Step 2 Install your PostgreSQL Database Server
Review step 2
Get the pgadmin client for your Linux/Mac desktop it will be used later on in the Quest.

Install the stand alone and independent Postgres:

ipkg install postgresql

READ the text after the install is finished!

mv /opt/etc/init.d/S98postgresql /usr/local/etc/rc.d/S22postgresql.sh

Do not use the /opt/etc/init.d/ for starting & stopping Postgresql, init.d only start services but does not stop them correctly!. It might destroy your database if it is not shutdown properly!

Since there is already a Postgres running internally we are going to move the postgres port from 5432 into 54320.

vi /opt/var/pgsql/data/postgresql.conf

Change the line that reads:

port = 5432

and change it into:
port = 54320

Consider, Setting the listen_addresses='*' and

edit the pg_hba.conf for remote access and add your desktop ip ( for example) to the file some thing like:
host    all         all            trust

Restart Postgresql
/usr/local/etc/rc.d/S22postgresql.sh restart

Use pgadmin to connect to your postgres database
(hint! postgresql port is @54320 not the default port @5432 ;-) that's the system's database)

Step 3 Create your JIRA Database in PostgreSQL
Read and apply step 3
No changes needed for the Synology.

Step 4 Install JIRA
Preprerations, creating the user & environment:

vi /etc/passwd
add the line:

vi /etc/shaddow
add the line:

vi /etc/group
add the line:

We don't use the installer, we need to manual install it.
Go to the download centre and get the tar.gz 32b version:
Download the file and unpack it.

mkdir /volume1/@atlassian
cp ~/atlassian-jira-4.4.tar.gz /volume1/@atlassian
cd /volume1/@atlassian

copy the JIRA tar into the directory and unpack.
tar zxvf atlassian-jira-4.4.tar.gz

Rename and chown the directory
mv atlassian-jira-4.4-standalone/ jira

chown -R jira:atlassian jira

set the JIRA_HOME
mkdir /volume1/@atlassian/application-data/
chown jira:atlassian
chmod 770

vi ./atlassian-jira/WEB-INF/classes/jira-application.properties
jira.home = /volume1/@atlassian/application-data/jira

Adjust the start and stop script
vi /volume1/@atlassian/jira/bin/start-jira.sh
vi /volume1/@atlassian/jira/bin/stop-jira.sh

change the first line in both start-jira.sh and stop-jira.sh

Change in both files also the line:

Check if this file su exists.

Also set your timezone correct, (see also the topic BUG Workaround here)

Find the line that reads: JVM_SUPPORT_RECOMMENDED_ARGS="" 
And add -Duser.timezone= with your time zone in the Canonical ID format.
For example Amsterdam would be:

Set the default user for the process:
vi /volume1/@atlassian/jira/bin/user.sh
Change the line:
JIRA_USER="jira" ##
( yes it says don't edit, do it anyway )

Create a rc.d script that starts/stops JIRA:
vi /usr/local/etc/rc.d/S95jira.sh


# JIRA Linux service controller script
# Set private environment, check if they apply for you.



cd "/volume1/@atlassian/jira/bin"

case "$1" in
        echo "Usage: $0 {start|stop}"
        exit 1

chmod 755 /usr/local/etc/rc.d/S95jira.sh

Now reboot your NAS and see if the services Postgres & Jira come up
http://<your NAS ip>:8080/

Integrating Jira with Apache on HTTP *:80
Open the server.xml file and adjust:
vi /volume1/@atlassian/jira/conf/server.xml

Find the line that reads:
<Context path="" docBase="${catalina.home}/atlassian-jira" reloadable="false" useHttpOnly="true">

And change it into:
<Context path="/jira" docBase="${catalina.home}/atlassian-jira" reloadable="false" useHttpOnly="true">

Now create a new file:
vi /usr/syno/apache/conf/jira-mod_proxy

And place the following content in it:

LoadModule proxy_module modules/mod_proxy.so
LoadModule proxy_ajp_module modules/mod_proxy_ajp.so
LoadModule proxy_http_module modules/mod_proxy_http.so

<Proxy *>
   Order deny,allow
   Allow from all

 ProxyRequests       Off
 ProxyPreserveHost On
 ProxyPass           /jira       http://localhost:8080/jira
 ProxyPassReverse    /jira       http://localhost:8080/jira

Write the file to: /usr/syno/apache/conf/jira-mod_proxy

Now open the file:
vi /usr/syno/apache/conf/httpd.conf-user

And add a last line:
Include conf/jira-mod_proxy   

Reboot your NAS ( or /usr/syno/apache/bin/httpd -k restart )
And point your browser to:

http://<your host name>/jira

And enjoy what unfolds!

Integrating Jira with Apache on HTTPS: *:443

Client Browser --> HTTPS --> Apache proxy --> HTTP --> Tomcat/JIRAFollow the steps in this document how to set up:Atlassian: Integrating+JIRA+with+Apache+using+SSL

vi /volume1/@atlassian/confluence/conf/server.xml
Add the last three lines to the connector and change the port into 8080

Connector port="8080" protocol="HTTP/1.1"

               <!-- The below are new lines to add - the above is untouched -->

Import your public key into the java key store and restart confluence:

Atlassian: Integrating+JIRA+with+Apache+using+SSL

Create a new file for httpd:
vi /usr/syno/apache/conf/jira-ssl.conf
And place the following content in it:

# Jira Proxy Setup
# J.W. de Roode Sep11

LoadModule proxy_module modules/mod_proxy.so
LoadModule proxy_ajp_module modules/mod_proxy_ajp.so
LoadModule proxy_http_module modules/mod_proxy_http.so

LoadModule ssl_module modules/mod_ssl.so
Listen 443

AddType application/x-x509-ca-cert .crt
AddType application/x-pkcs7-crl    .crl

SSLPassPhraseDialog  builtin

SSLSessionCache          none
SSLSessionCacheTimeout   3600

SSLMutex  file:/var/tmp/ssl_mutex-user

SSLProtocol all -SSLv2
SSLCertificateFile /usr/syno/etc/ssl/ssl.crt/server.crt
SSLCertificateKeyFile /usr/syno/etc/ssl/ssl.key/server.key

## SSL Virtual Host Context

<VirtualHost *:443>

  SSLEngine on

  <FilesMatch "\.(cgi|shtml|phtml|php)$">
      SSLOptions +StdEnvVars

  BrowserMatch ".*MSIE.*" \
         nokeepalive ssl-unclean-shutdown \
         downgrade-1.0 force-response-1.0

  CustomLog /dev/null \
          "%t %h %{SSL_PROTOCOL}x %{SSL_CIPHER}x \"%r\" %b"

  <Proxy *>                                                                                                                       
    Order deny,allow                                                                                                                
    Allow from all                                                                                                                  

  ProxyRequests       Off
  ProxyPreserveHost   On
  ProxyPass /jira http://localhost:8080/jira
  ProxyPassReverse /jira http://localhost:8080/jira


Open the file:
vi /usr/syno/apache/conf/httpd.conf-user

And add/replace the last lines:
#Include conf/jira-mod_proxy # HTTP  Config
Include conf/jira-ssl.conf   # HTTPS Config

Reboot your NAS ( or /usr/syno/apache/bin/httpd -k restart )
And point your browser to:

https://<your host name>/jira

And enjoy what unfolds!

Follow-up on the Dragon Quest assignments of stage 1 and Tweet the completion on twitter.

Dragon Stage 2 - Set Up GreenHopper in JIRA
Follow the steps in the document of Stage 2 of the Dragons.

Next post will handle stage 3 - Install Confluence