Mesos Cluster Setup

This ansible playbook setup a mesos cluster with high availability based on this guide. Also it setups a development environment for running a galaxy instance.

Inventory Configuration

You have to configure your inventory to specify the hosts belonging to every group. This playbook requires four groups of hosts:

• nfs_server: An nfs server.
• nfs_clients: List of hosts which share a directory with nfs sever.
• mesos_masters: The list of mesos_masters to manage the cluster. One of them is the leader master elected by Zookeeper and the rest are standby.
• mesos_slaves: The list of mesos_slaves nodes.
• chronos: Hosts that run chronos framework. Note that chronos is not supported on Ubuntu 16.04.
• galaxy: A host running Galaxy instance.
• docker-registry: A host running a private Docker registry.

Perhaps, you may also want to specify additional group variables based on your host, e.g. change the ansible_python_interpreter variable to use python3.

Setup

Install any required playbooks:

sudo ansible-galaxy install -r requirements.yaml

Setup cluster and Galaxy:

ansible-playbook -i hosts site.yaml

Use Case: Run SADI workflow on a Mesos cluster

This guide is tested on VMs running Ubuntu 14.04 with 4GB of RAM and quad core processor. Also, our cluster consists of the following VMs (not constrictive though):

• One VM running NFS server
• One VM running Galaxy
• One VM running Chronos and mesos-master
• One VM running mesos-slave
• One VM running docker registry

First, add the following variables to the group_vars/galaxy:

galaxy_repo: ssh://phab-vcs-user@phab.dev.grnet.gr:222/diffusion/GALAXY/galaxy.git
galaxy_version: feature-chronos

When Ansible clones Galaxy, these variables are used to determine the Galaxy repository and branch. Ensure that you have access to the phabricator from the corresponding host.

Then, export the following variable to forward ssh agent to your host:

export  ANSIBLE_SSH_ARGS="-o ForwardAgent=yes"

On the host which runs galaxy, create the following job configuration on <galaxy_repo>/config/job_conf.xml (Do not forget to change the parameter of chronos-master to point to the host which runs your chronos):

Also, note that you need your site certificate and its key to be already defined at location conf/domain.crt and conf/domain.key> respectively (relative to server_root variable-see below) to setup docker_registry successfully.

<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
<job_conf>
    <plugins>
        <plugin id="chronos" type="runner" load="galaxy.jobs.runners.chronos:ChronosJobRunner" workers="4">
            <param id="chronos">{{ chronos-host:8080 }}</param>
            <param id="owner">galaxy@foo.test</param>
        </plugin>
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
    </plugins>
    <handlers>
        <handler id="main"/>
    </handlers>
    <destinations default="local_dest">
        <destination id="chronos_dest" runner="chronos">
            <param id="docker_enabled">true</param>
            <!-- Directory which hosts working directories of Galaxy. -->
            <param id="volumes"{{ directory }}</param>
            <param id="docker_memory">512</param>
            <param id="docker_cpu">2</param>
            <param id="max_retries">1</param>
        </destination>
        <destination id="local_dest" runner="local">
            <param id="docker_enabled">true</param>
            <param id="docker_sudo">false</param>
        </destination>
    </destinations>
    <tools>
        <tool id="SADI-Docker-sadi_client" destination="chronos_dest"/>
        <tool id="SADI-Docker-RDFSyntaxConverter" destination="chronos_dest"/>
        <tool id="SADI-Docker-mergeRDFgraphs" destination="chronos_dest"/>
        <tool id="SADI-Docker-rapper" destination="chronos_dest"/>
        <tool id="SADI-Docker-tab2rdf" destination="chronos_dest"/>
    </tools>
</job_conf>

Then restart galaxy and run workflow as described here.

Defaults variables per role.

Below, there is a list of default variables per role. You can override them by setting your variables on your group_vars directory. Ensure that object_story_directoy and mountable_dir points to the same directory.

Role: nfs

# NFS export options.
export_options: rw,sync,no_subtree_check,no_root_squash

Role: nfs_clients

mountable_dir: /root/galaxy_workspace

Role: common

# Mesosphere apt repo.
mesosphere_repo: "deb http://repos.mesosphere.com/{{ ansible_distribution | lower }} {{ ansible_distribution_release }} main"

Role: mesos_masters

# Size of Zookeeper Quorum
quorum_size: 1

Role: chronos

chronos_http_port: 8080
chronos_https_port: 9443

Role: galaxy

# Directory to host galaxy code.
galaxy_directory: /srv/galaxy

# Directory which holds object store data. This directory is mounted to an nfs
# server.
object_store_directory: /root/galaxy_workspace

# Directory which is the galaxy job working directory. It's parent is
# `object_store_directory`.
job_working_directory: jobs_directory

# Directory which holds datasets of workflows. It's parent is
# `object_store_directory`.
files_directory: files

# tmp directory of jobs. It's parent is `object_store_directory`.
tmp_directory: tmp

# Galaxy remote repo.
galaxy_repo: https://github.com/galaxyproject/galaxy

# Version of the repository to check out. A branch, a tag or a commit hash.
galaxy_version: feature-chronos

# True if SADI workflow should be installed.
install_sadi: True

# Directory to host SADI code.
sadi_directory: /root/SADI

Role docker-registry

# Credentials for registry
registry_username: openminted
registry_password: OpenMinTeD

# Server root needed for apache.
server_root: /usr/local/apache2