How to build a WormBase Virtual Machine
- 1 Overview
- 2 Base Virtual Machines
- 3 About the WormBase core virtual machines
- 4 Directory structure of the Virtual Machines
- 5 Updating the software
- 6 Building virtual disks for a new release
- 7 Virtual Machine exceptions
- 8 Updating the software after distribution
WormBase Virtual Machines are created for each release of the database. This process is almost entirely scripted, created from base virtual machines that run all the time and are automatically kept up-to-date with the production nodes.
To simplify the download and update process, WormBase virtual machines are split into modules. The primary virtual machine contains all software and configuration running under CentOS 5 (for servers) or Ubuntu 6.06 (for desktops). Databases are maintained as virtual disks (VMDKs).
Creation of a new VM requires three steps:
1. Syncing the software to the staging rsync module hosted on the main WormBase development site.
2. Creation of VMDKs for available databases.
3. Tarring and gzipping.
The process is described in more detail below.
Base Virtual Machines
The base virtual machines are located at:
wormbase-live-server : CentOS 5, configured in particular for server use IP: 192.168.20.100
wormbase-live-desktop : Ubuntu 6.06 IP: 192.168.
About the WormBase core virtual machines
Core virtual machines are essentially production nodes virtualized. This makes them very convenient for development, testing, and even stop-gap emergency server recovery. The key differences between production nodes and the core virtual machines are:
- Database are maintained as virtual disks instead of in the main virtual machine itself.
- Perl libraries are maintained in private directories (/usr/local/wormbase/extlib), with corresponding modifications to perl.startup. This allows me to push new modules onto existing virtual machine installations with ease.
I maintain two variations of the WormBase virtual machines.
wormbase-live-desktop: Operating system: Ubuntu 6.06-desktop
wormbase-live-server: Operating system: CentOS 5
The WormBase core virtual machines
To fetch the IP address for a virtaul machine, log on to the appropriate host, then:
vmware-cmd <cfg> getguestinfo "ip"
Directory structure of the Virtual Machines
Since databases are maintained as virtual disks, the virtual machine needs to know where to find them in order to launch. For the core virtual machine, the directory structure looks like this:
wormbase-live-server/wormbase.vmx WS180-database/acedb.vmdk /elegans_gff.vmdk /briggsae_gff.vmdk /remanei_gff.vmdk /autocomplete_gff.vmdk /support.vmdk current_databases -> WS180-databases
Thus, the virtual machine expects the databases to be located at :
Updating the software
Software on the base virtual machines is kept in sync with the shell script ~wormbase/bin/pull_software.sh. This script syncs to the production nodes every day and is set to run under non-privileged cron every day.
* 2 * * * /home/wormbase/bin/pull_software.sh
Building virtual disks for a new release
Shutdown the core virtual machine:
vmare-cmd <cfg> shutdown
Run the prepare_virtual_machine.sh script:
This will set up a directory structure like this and untar some empty VMDKs:
wormbase-live-server/wormbase.vmx WSXXX-databases/ current_databases -> WSXXX-databases
Logon to the core virtual machine
Virtual Machine exceptions
To make creation and maintenance of virtual machines easier, I've changed some of the default settings in the core machines.
1. Acedb database location
WormBase core VMXs
This requires a corresponding modification in the xinetd configuration.
2. MySQL datadir
WormBase core VMXs
3. Support databases
WormBase core VMXs
/mnt/support_databases /usr/local/wormbase/databases -> /mnt/support_databases
Updating the software after distribution
Once distributed Wormbase virtual machines can be kept up-to-date by a simple script. This has several advantages.
1. It keeps download sizes small
2. It keeps local configuation from being rewritten with every update.
3. It modularizes required databases so that users can choose what databases they wish to install.
Establishing the Virtual Machine
Build and install VMware Server (currently vers 1.0.3)
cd ~/build tar xzf ../src/vmware-server-1.0.3.tar.gz sudo ./vmware-install.pl
For WormBase, I place the virtual machines in /usr/local/vmx.
Installing the OS
Fetch a suitable ISO. From the console interface, edit options for the CD-ROM. Attach the ISO and make sure the "Connect on Startup" option is checked.
Users and groups
WormBase virtual machines have a slightly different user and group arrangment than we have traditionally used.
The main user is WormBase User:
Login: wormbase pass: wormbase home: /home/wormbase
To keep things copacetic with WormBase proper, I've created a symlink: /usr/local/wormbase -> /home/wormbase
Preparing a VMX for release
1. Start the guest OS.
2. In the guest, purge things like access logs, tarballs, etc
3. Shrink the disk in the disk by first zeroing empty space
sudo dd if=/dev/zero of=/empty_file rm /empty_file
4. Set the VMX to graphical runlevel 5 (/etc/inittab)
5. Shutdown the guest
6. Copy the current wormbase-live to a directory named by release:
cp -r wormbase-live wormbase-WSXXX.YYYY.MM.DD
7. In the console, set the version and release date
WormBase (WSXXX; DD Feb YYYY)
8. Defragment the disk from the VMWare console:
Edit options > Hard Disk > Defrag the disk
9. In the VMWare console, set networking to NAT (assume desktop usage) and restart the guest.
10. Start the new VMX.
11. Reset the MAC address
12. Finish shrinking the disk using the vmware-toolbox:
$ vmware-toolbox (select shrink)
13. When complete, shut down the VMX
tar czf wormbase-WSXXX.YYYY.MM.DD.tgz
15. Symlink to make it available via http
cd /usr/local/wormbase/html/vmx ln -s /usr/local/vmx/wormbase-WSXXX.YYYY.MM.DD.tgz wormbase-WSXXXX.YYYY.MM.DD.tgz
16. Upload the new VM to BitTorrent
17. Update the [[Virtual_Machines Virtual Machines] page on the Wiki
Configuring VMXs as hosted frozen releases
To use a Virtual Machine as a server, a few small modifications need to be made.
1. From the VMWare Server console, launch the virtual machine
2. Set a static IP (must be assigned!)
In this example, the guest OS IP is 184.108.40.206. This should be changed to whatever your assigned IP address is.
ifconfig eth0:0 220.127.116.11 netmask 255.255.255.0 broadcast 18.104.22.168 route add -host 22.214.171.124 dev eth0
You can also do this from the GUI if you prefer, under System Settings -> Network. Double click on the network adaptor.
Address: Your assigned IP address Subnet mask: 255.255.255.0 Default gateway: 126.96.36.199 Broadcast host: 188.8.131.52 (not explicitly set in the GUI)
3. Reset the MAC ID of the guest
System Tools > Network
Double click on the network adaptor and select the "Hardware" tab. Click on "Probe", then "OK"
4. Add the following lines to /etc/resolve.conf for DNS
search cshl.edu nameserver 184.108.40.206 nameserver 220.127.116.11
5. Set the hostname
This can be done either in the GUI under the Network panel, or using the following command line terms.
If you have a static IP address, then /etc/hosts is configured as follows:
127.0.0.1 localhost.localdomain localhost 143.488.220.44 mybox.mydomain.com mybox
After updating the /etc/hosts file correctly, the "hostname" command should be run as follows to set your hostname:
6. Edit /usr/local/wormbase/conf/localdefs.pm and httpd.conf with the appropriate hostname
8. Shutdown the virtual machine and copy it as a backup
I append "server" to the name to indicate that it is configured as a server
tar czf wormbase-WS100.2003.05.13-server.tgz wormbase-WS100.2003.05.13