Helpful Tips for Newbie System Admins

Before you start reading this tutorial, let me remind you once again who the intended audience of this post is — newbie system administrators. If you’re an experienced admin and are going to laugh at my naivete for writing such basic stuff, please go away — or provide some more ‘advanced’ tips in the comments below so that I know better for the future.

Anyway, let’s begin. If you’re like most newbie system admins, you run a windows system on your home PC / work laptop and connect to the servers you’re managing using putty. Everyone uses putty, you say. Well, yes but there are alternatives. One of the things I hate is to have to copy/paste all the usernames and passwords into that putty session before I can login. So, let’s get rid of that first.

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Installing Jira with MySQL

Jira is an extremely well-known issue tracking system and is used widely for project management in a wide array of fields. It has quite a detailed documentation but it’s in the form of a wiki and as we all know, wikis are the worst way of creating software documentation. Anyway, in order to install Jira with MySQL, you will have to click and click and click. This tutorial aims to ease this issue by providing step-by-step instructions on how to install jira and enable it to connect with MySQL for storage. So let’s begin.

Note: These instructions are for the standalone version of Jira. You can use them quite easily for the WAR/EAR version but if you’re going on that route, you probably don’t need this article.

Ok, first download and install Java (I usually go with JDK) — version 6 is preferred. You can get the .bin file for Linux from (I refuse to call it Oracle Java). Make it executable and run it. JDK will be extracted in your current directory. Move it to /usr/share. Then set the JAVA_HOME variable.

export JAVA_HOME

You might want to set this in your ~/.bash_profile file.

Next, create a user with which we will start jira — for security reasons.

sudo /usr/sbin/useradd --create-home --home-dir /usr/local/jira --shell /bin/bash jira

Download and extract the jira standalone .tar.gz file to /usr/local/jira and change ownership of all the files to the jira user:

chown jira:jira /usr/local/jira -R

Open port 8080 which is used by jira (by default) — edit the file /etc/sysconfig/iptables and enter the following rule:

-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 80 -j ACCEPT

Set the required jira.home property in the file /usr/local/jira/atlassian-jira/WEB-INF/classes/

mkdir /usr/local/jira/jirahome
vi /usr/local/jira/atlassian-jira/WEB-INF/classes/
# set the variable jira.home to /usr/local/jira/jirahome

Restart the firewall and start jira using the following command:

sudo -u jira nohup /usr/local/jira/bin/ run & > jira-nohup.log

The use of sudo will run jira as the user jira and nohup will ensure that jira won’t stop running as soon as you close the shell. The output produced by the command will be saved to jira-nohup.log

Open the browser on location http://your.ip.add.ress:8080/ and ensure that you can see the jira setup page. Don’t bother proceeding with the setup because as soon as we connect jira to MySQL, this information will be lost. Let’s do that now.

Connecting with MySQL

Begin by stopping jira, installing mysql server, setting it to always start on system startup and starting the server.

yum install mysql mysql-server 
chkconfig mysql on 
service mysqld start 

Then start mysql, create a database and user for jira and assign all rights to the new user on the new database.

create database jiradb character set utf8;
grant all privileges on jiradb.* to jira@localhost identified by '[your new password]';

Now, edit the conf/server.xml in the jira directory and change the data source as follows:

<Resource name="jdbc/JiraDS" auth="Container" type="javax.sql.DataSource"
            password="[jira user password]"
            validationQuery="select 1"/>

Note that the ampersand code in the connection string is not a formatting problem. It really has to say amp with an ampersand and a semicolon at either end.

Finally, edit the atlassian-jira/WEB-INF/classes/entityengine.xml file to set the final attribute:

<datasource name="defaultDS" field-type-name="mysql"
      use-foreign-keys="false" ...

Delete the schema-name="PUBLIC" attribute immediately after the changed line to ensure that the database is populated properly.

Start jira once again and now you can enter the setup information. Open MySQL and ensure that jira is, in fact, using this engine.

Creating Multiple Volumes on Amazon EC2

For those of you who have used Amazon AWS (EC2 specifically) for more than just testing would know that the / partition in an AMI does not go beyond 10GB. So, if you need more space you need to mount more volumes. This is a beginner’s guide to do just that.

First off, create an AMI with EBS storage type and take a note of the zone in which that AMI sits. You can find this through the details pane in the ‘instances’ section of your AWS management console. Then, go over to the ‘volumes’ section and create a new volume.

Here, you need to make sure that you create the volume in the same zone as your AMI or you won’t be able to use the volume with it. Specify the capacity of the volume. That’s all that’s required at this stage. Click create and wait until the new volume becomes available. Then right-click on the volume and ‘Attach Volume’. Make sure you select the right instance and then specify the new device name. You can use something like ‘/dev/sdd’. Just use fdisk -l in your running instance to make sure it’s not already in use.

After that, login to your AMI and fdisk -l again to make sure that the new volume is available. Now, you need to create a partition and format it for linux to use. Then, mount it someplace. Here we’re going to move the whole /var to this new partition so that our logs etc can have more free space to grow.

mkfs.ext3 /dev/sdd 
mkdir /mnt/var
mount /dev/sdd /mnt/var 
cp -R /var/* /mnt/var
touch /mnt/var/new-vol

The last line is there to verify after boot that you are indeed using the newly volume. You can also use df -h after reboot to test this but I just feel better this way.

Finally, open up the /etc/fstab file and enter the new device /dev/sdd and the mount point /var.

/dev/sdd    /var    ext3     defaults    0    0

And reboot.