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ICGC DCC - Ansible

Ansible scripts for provisioning ETL, Portal, Downloader and Submission systems

Requirements:

1. Install Ansible

Easiest way for MacOSX to get the latest Ansible is using Homebrew:

Note: Ansible version should be at least 1.9

$ brew install ansible

For other platforms, refer to Ansible documentation.

2. Install Open Stack shade client.

$ sudo pip install shade

They install the required dependencies, but you might need to install additional clients from here.

3. Provide the settings.

Create a new file, vars/main.yml using vars/main.yml.template as template, providing necessary settings.

Furthermore, there are several variables that need to be set in: group_vars/vars/main.yml

  • Proxy
  • http_proxy
  • External URLs
  • external_submission_url
  • external_docs_url
  • Misc
  • icgc_url
  • Contact
  • smtp_server
  • sender
  • recipients

4. (Optional) Edit ssh config

Edit /etc/ssh_config and add the following to avoid having to accept connecting to each server.

Host 10.5.74.*
	StrictHostKeyChecking no
	UserKnownHostsFile=/dev/null

Run

Execute the following command:

You can also execute playbooks individually:

$ ansible-playbook -i config/hosts submission.yml

Extra Tips and Notes:

Ansible in memory inventory

During the running of a playbook, our tasks and roles are configured to add new groups of hosts to the in memory inventory.

For the following explanations, we will use the first few lines of the download.yml playbook as an example:

- include: tasks/setup.yml group=hadoop-master:hadoop-worker:download
- include: tasks/setup-existing.yml group=hadoop-master:hadoop-worker:download

  • all_instances - All hosts from all groups that are either being provisioned and/or used are lumped together into a single host group. The purpose of this group is so we can write out the hostname and ips of every server to the /etc/hosts file of every server. This way, every server, knows about every other server.

  • We do some parsing of host names to generate groups of related servers based on the the way they are named. For example, in the hadoop-worker group we have the hostnames dcc-hadoop-worker-[1:2]. A group called hadoop_worker is created containing the hosts dcc-hadoop-worker-1 and dcc-hadoop-worker-2. The utility of this becomes more obvious when you look at groups and playbooks that use a wider array of servers with different purposes, such as the portal.yml playbook with the portal host group.

Data

The playbooks do not load any production data into either Elasticsearch or Postgres. This is left up to the user.

Hosts

Ensure that the host images for the openstack instances provide enough resources. The hosts provisioned by the playbook in testing had the following configuration
OS Ubuntu 12.04
RAM 16GB
# CPU 8
Storage 160GB

HDFS & Spark

It is a good idea that once the hadoop cluster is provisioned, that you inspect the web UI of the NameNode/Master to ensure the nodes are up and their services are enabled. The created NameNode can easily provision more RAM than you provided it, so that is something to be aware of. Also ensure the configuration on the nodes is not stale.

Software

All downloaded software from ICGC comes with install scripts. Should you require a more up to date version of any of the software, the install script should provide you with the functionality to update the software.

Example installing a specific version:

$ ./install -r 4.0.4

TODOs:

A list can be found here.

Misc

Java Install

Installs the latest Oracle Java 8 using PPA repository.

  • Create a custom playbook
- name: Installs Oracle JDK with PPA
  hosts: all
  gather_facts: no
  sudo: yes
  roles:
    - jdk-ppa
  • Create a custom hosts file
[java]
127.0.0.1
  • Run the playbook
ansible-playbook -i java_hosts java.yml