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NSWI106-screencast

Introduction

Final task for the NSWI106 - Linux Administration course. Setup of Apache spark cluster using Vagrant and Ansible.

What is Vagrant?

Vagrant is a tool for building and managing virtual machine environments in a single workflow. With an easy-to-use workflow and focus on automation, Vagrant lowers development environment setup time, increases production parity, and makes the "works on my machine" excuse a relic of the past.

Vagrant provides easy to configure, reproducible, and portable work environments built on top of industry-standard technology and controlled by a single consistent workflow to help maximize the productivity and flexibility of you and your team.

Source: Vagrant intro

What is Ansible?

Ansible is an open-source software for provisioning, configuration management, and application-deployment tool enabling infrastructure as code.

Source: Ansible wiki

What is Spark?

Apache Spark is a unified analytics engine for large-scale data processing. It provides high-level APIs in Java, Scala, Python and R, and an optimized engine that supports general execution graphs. It also supports a rich set of higher-level tools including Spark SQL for SQL and structured data processing, MLlib for machine learning, GraphX for graph processing, and Structured Streaming for incremental computation and stream processing.

Source: Spark overview

Installation

In this screencast we will be using a Linux environment. However, the tools we use are relatively OS agnostic, so there shouldn't be many problems applying these steps to a different architecture.

Firstly, we will have to install the required tools, i.e. vagrant and ansible. Both tools are quite popular and should be available in the repositories every major distributions package manager. Otherwise, please refer to their respective install pages.

As a default hypervisor Vagrant uses VirtualBox, we however want to utilize the native linux KVM through libvirt. Vagrant unfortunately doesn't support it out-of-the box, but fortunately is the vagrant-libvirt plugin available. Installing it can be as simple as:

> vagrant plugin install vagrant-libvirt

Note, that this is a third-party solution and the above step may not work correctly in every environment. Please consult the vagrant-libvirt installation guide

If you wish to use a different hypervisor you are free to do so. As you will see switching switching a hypervisor in Vagrant is trivial.

Architecture

We will setup a simple Spark cluster with one master (control) node and several worker nodes all connected and managed by the master. All will be connected on the same network.

We will assign IP addresses as follows

node IP
master 192.168.50.10
worker-01 192.168.50.11
worker-02 192.168.50.12
...
worker-XX 192.168.50.(10 + XX)

For cluster management we will use the Spark in the simple Standalone mode. To read more about cluster management options, please refer to the Spark Cluster Mode Overview

Vagrant setup

We create a new directory named spark_example where we will store our setup.

For our purposes, we will setup our virtual machines using vagrant. We will use the debian/buster64 box (virtual machine image) provided by the community. More boxes can be found on the official Vagrant site.

To create the initial configuration file we can simply run

> vagrant init debian/buster64
A `Vagrantfile` has been placed in this directory. You are now
ready to `vagrant up` your first virtual environment! Please read
the comments in the Vagrantfile as well as documentation on
`vagrantup.com` for more information on using Vagrant.

This will create a new file named Vagrantfile in the current working directory. This file contains a lot of comments with tips and example configurations.

Vagrant uses ruby for writing configuration files, but for basic setups the knowledge of ruby is not required.

You can now run vagrant up and vagrant will download the requested box for you and start up the VM. You can access the VM through SSH with the vagrant ssh command. If you are done using your machine, you can turn it off with vagrant halt or save its state with vagrant suspend. If you wish to permanently delete your machines it use vagrant destroy.

spark_example/Vagrantfile

We will be starting with the following:

# frozen_string_literal: true

# -*- mode: ruby -*-
# vi: set ft=ruby :

VAGRANTFILE_API_VERSION = '2'
BOX_IMAGE = 'debian/buster64'

Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
    config.vm.box = BOX_IMAGE
end

As you can see, the amount of configuration required to setup a VM with Vagrant is minimal.

Multi-machine setup

Next, we will setup a multi-machine environment connected using a private network. With Vagrant we are able to do that with only few lines of code.

Every time you plan to make a bigger change to your configuration be sure to run vagrant destroy -f to delete your machines first. Sometimes vagrant can start from a changed configuration with only vagrant reload, but in the early testing stages it is much easier to create your VMs from scratch.

We will create a multi-machine environment with the following configuration:

# frozen_string_literal: true

# -*- mode: ruby -*-
# vi: set ft=ruby :

VAGRANTFILE_API_VERSION = '2'

# How many slave nodes we want to create
WORKER_COUNT = 4

# Default box to use
BOX_IMAGE = 'debian/buster64'

# Default starting address
IP_START = 10

Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
  # Create the master node
  config.vm.define 'master', primary: true do |subconfig|
    subconfig.vm.box = BOX_IMAGE

    # Connect master to a private network
    subconfig.vm.network :private_network, ip: "192.168.50.#{IP_START}"

    # Set hostname for master
    subconfig.vm.hostname = 'master'
  end

  # Create the worker nodes
  (1..WORKER_COUNT).each do |machine_id|
    # Name of the node in format "worker-01", "worker-32", etc.
    box_name = "worker-" + machine_id.to_s.rjust(2, "0")

    # IP address of the worker
    box_ip_address = "192.168.50.#{machine_id + IP_START}"

    # Setup one slave node
    config.vm.define box_name do |subconfig|
      subconfig.vm.box = BOX_IMAGE

      # Connect a worker to a private network
      subconfig.vm.network :private_network, ip: box_ip_address

      # Set worker hostname
      subconfig.vm.hostname = box_name
    end
  end
end

Here, we did a number of things.

  1. Because we wanted to extend the configuration the master node, we defined a new node 'master' and started a new configuration block:

    # Create the master node
config.vm.define 'master', primary: true do |subconfig|
    # ... rest of the configuration
end

    Here we can use the subconfig variable and all the options will be tied only with the master node.

    Also note that we defined this node with primary: true. We will get to that shortly.

  2. We connected the node to a private_network and assigned it the 192.168.50.10 IP address with the line:

    # Connect master to a private network
subconfig.vm.network :private_network, ip: "192.168.50.#{IP_START}"

    We used to ruby string interpolation syntax #{}.

    We also assigned the node a unique hostname:

    # Set hostname for master
subconfig.vm.hostname = 'master'

  3. Next, we added the worker nodes with the following loop

    (1..WORKER_COUNT).each do |machine_id|
  # ... worker configuration
end

    Note that the standard ruby for loop does not work. See looping over VM definitions.

    The rest of the configuration is similar to the configuration of the master node.

You can now vagrant up to create your machines. Note that there is a small change in some of vagrant commands in multi-machine setups. For example to vagrant ssh into a machine you have to explicitly specify the machine name as defined in the vagrant configuration. So vagrant ssh worker-01 would connect you to the first node. However, you can define one of your machines to be primary which will be the default option when running vagrant ssh. We did exactly that with the master node.

You should now be able to connect to the master node by running vagrant ssh (without additional arguments) and from there ping other VMs on the network.

vagrant > ping 192.168.50.11
PING 192.168.50.11 (192.168.50.11) 56(84) bytes of data.
64 bytes from 192.168.50.11: icmp_seq=1 ttl=64 time=0.406 ms
64 bytes from 192.168.50.11: icmp_seq=2 ttl=64 time=0.400 ms
64 bytes from 192.168.50.11: icmp_seq=3 ttl=64 time=0.453 ms
...

Configuring the provider

We also want to tell vagrant about the system resources we want assign to our machines. We will do that globally with the config.vm.provider option.

# ... other variables
VAGRANTFILE_API_VERSION = '2'

# Parameters of the created VMs
VM_MEMORY = 6144
VM_CPUS = 8

Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|

  # ... VM configuration

  # Tell vagrant about system resources we want to use
  config.vm.provider :libvirt do |libvirt|
    # Customize the amount of memory on the VM:
    libvirt.memory = VM_MEMORY

    # Customize the number of cpus on the VM:
    libvirt.cpus = VM_CPUS
  end

end

Here we specified that we wish to use the libvirt provider and assigned the desired amount of memory and CPUs.

Disabling default NFS sharing

By default vagrant also mounts the current working directory as NFS drive to the VM. We disabled this behaviour by adding this line at the end of the configuration.

# Disable mounting the default vagrant folder
config.vm.synced_folder '.', '/vagrant', disabled: true

Provisioning

For provisioning we will be using Ansible. Ansible configuration is done via configuration files written in YAML called playbooks. Playbooks contain a list of so-called plays which are essentially groups of tasks you want to execute. Tasks are are composed of modules which are usually the most atomic parts of your playbooks.

A simple playbook might look something like this:

--- # Three dashes signify YAML file, Ansible doesn't care if you forget them though
- name: My first play.
  hosts: all
  tasks:
    - name: "My first task!"
      debug: "msg=Hello from VM - {{ inventory_hostname }}"

- name: My second play!
  hosts: all
  become: True  # get superuser privilages
  tasks:
    - name: Notify user about what I want to do
      debug:
        msg: I'm going to install packages

    # ... tasks for installing a package

    # The `name` field is optional (but improves readability).
    - debug: msg="packages are installed."

We will get to the structure of an ansible-playbook shortly. For now you can go ahead and add the contents of this file to setup-spark.yml. We will use it as a base for provisioning.

We will modify the Vagrantfile by adding the following lines to the configuration.

# ... other variables

# Playbook to run for provisioning
PLAYBOOK = 'setup-spark.yml'

Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|

  # ... rest of the configuration

  config.vm.provision :ansible do |ansible|
    # Disable default limit to connect to all the machines
    ansible.playbook = PLAYBOOK
  end
end

You can now create your VMs, Vagrant you will see Vagrant run ansible and provision them for you. You will also notice that the VMs are being provisioned one after another (you can check that by running vagrant provision). This is actually something we don't want because ansible is capable (and expected) to run the individual plays in parallel.

To our knowledge there isn't currently a "clean" way configure Vagrant to run the provisioning only after booting all the machines. There is however, a small "hack" that can achieve this. You run the provisioning from the last created machine only and turn off the default limit for provisioning (which is current machine only). This also endorsed by Vagrant documentation.

We modify the Vagrantfile followingly:

(1..WORKER_COUNT).each do |machine_id|
  # ... worker variables

  # Setup one slave node
  config.vm.define box_name do |subconfig|

    # Run ansible provisioning in parallel by running the provisiong from the
    # last created node only
    if machine_id == WORKER_COUNT
      subconfig.vm.provision :ansible do |ansible|
        # Disable default limit to connect to all the machines
        ansible.limit = 'all'
        ansible.playbook = PLAYBOOK
      end
    end
  end
end

If you run vagrant provision now, you should see all the machines provisioned in parallel.

There is now only a few last things we need to add to our Vagrant configuration.

Firstly, we want to create a group within ansible and assign all the workers to it. This will allow us to configure all the workers simultaneously.

We can do that by adding the following lines into the provisioning section:

ansible.groups = {
  'workers' => (1..WORKER_COUNT).map { |i| 'worker-' + id_number.to_s.rjust(2, '0') }
}

Finally, we want to notify ansible about the IP address it should use for configuration. This is needed in case the VMs have multiple network interfaces. We will use this variable ourselves when configuring ansible later. We can achieve this by defining the ansible.host_vars field in configuration ans supplying it a hash (ruby dictionary) with key-value pairs of hostname and value we want to set. The value is another hash containing the values we want to supply ansible.

We start by defining a new hash called spark_ip_addresses and filling it with the IP addresses for individual nodes like this:

# Define hash for master node
spark_ip_addresses = {
  'master' => {
    'spark_ip_address' => '192.168.50.10'
  }
}

# ... add new entry
spark_ip_addresses[box_name] = {
  'spark_ip_address' => box_ip_address
}

In the provisioning section we then provide the hash to the ansible.host_vars:

ansible.host_vars = spark_ip_addresses

Final Vagrantfile

The final Vagrantfile (with some minor improvements) looks like this:

# frozen_string_literal: true

# -*- mode: ruby -*-
# vi: set ft=ruby :

VAGRANTFILE_API_VERSION = '2'

# How many slave nodes we want to create
WORKER_COUNT = 4

# System resources for nodes
VM_MEMORY = 6144
VM_CPUS = 8

# Default starting host address
IP_START = 10

# Default box to use
BOX_IMAGE = 'debian/buster64'

# Playbook to run for provisioning
PLAYBOOK = 'setup-spark.yml'

# Generate a name for the worker based on its ID number
def worker_name(id_number)
  # Name of the node in format "worker-01", "worker-32", etc.
  'worker-' + id_number.to_s.rjust(2, '0')
end

Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
  # Create the master node
  config.vm.define 'master', primary: true do |subconfig|
    subconfig.vm.box = BOX_IMAGE

    # Connect master to a private network
    subconfig.vm.network :private_network, ip: "192.168.50.#{IP_START}"

    # Set hostname for master
    subconfig.vm.hostname = 'master'
  end

  spark_ip_addresses = {
    'master' => {
      'spark_ip_address' => "192.168.50.#{IP_START}"
    }
  }

  # Create the worker nodes
  (1..WORKER_COUNT).each do |machine_id|
    box_name = worker_name(machine_id)

    # IP address of the worker
    box_ip_address = "192.168.50.#{machine_id + IP_START}"

    # Setup one slave node
    config.vm.define box_name do |subconfig|
      subconfig.vm.box = BOX_IMAGE

      # Connect a worker to a private network
      subconfig.vm.network :private_network, ip: box_ip_address

      # Set worker hostname
      subconfig.vm.hostname = box_name

      spark_ip_addresses[box_name] = {
        'spark_ip_address' => box_ip_address
      }

      # Run ansible provisioning in parallel by running the provisiong from the
      # last created node only
      if machine_id == WORKER_COUNT
        subconfig.vm.provision :ansible do |ansible|
          # Disable default limit to connect to all the machines
          ansible.limit = 'all'
          ansible.playbook = PLAYBOOK

          ansible.host_vars = spark_ip_addresses

          ansible.groups = {
            'workers' => (1..WORKER_COUNT).map { |i| worker_name(i) }
          }
        end
      end
    end
  end

  # Tell vagrant about system resources we want to use
  config.vm.provider :libvirt do |libvirt|
    # Customize the amount of memory on the VM:
    libvirt.memory = VM_MEMORY

    # Customize the number of cpus on the VM:
    libvirt.cpus = VM_CPUS
  end

  # Disable mounting the default vagrant folder
  config.vm.synced_folder '.', '/vagrant', disabled: true
end

Ansible setup

Setting up an inventory

Firstly, we need to inform Ansible about the machines we wish to provision. This is done through what Ansible calls an inventory. In an inventory you specify the hosts Ansible should configure. Additionally, Ansible can group hosts into groups, so you can run related task for multiple nodes at once, which simplifies the configuration even further. The default inventory can be found in /etc/ansible/hosts.

We will be able to skip writing an inventory file entirely, because Vagrant is able to auto-generate the inventory file for us. After running vagrant up with provisioning using Ansible set up, you can find the auto-generated file in .vagrant/provisioners/ansible/inventory/vagrant_ansible_inventory in the root of your project directory.

Within, you should be able to see the hosts we defined in Vagrant with information how to connect as well as the spark_ip_address variable for each host. There should also be defined the workers group starting with [workers] and listing all the worker hostnames.

To test that the inventory file is working correctly we can run a one-off module using the ansible command. We will tell each machine to print its inventory hostname.

> ansible all \
    -i .vagrant/provisioners/ansible/inventory/vagrant_ansible_inventory \
    -m debug -a var=inventory_hostname

Here we tell vagrant to run the debug module printing the inventory_hostname variable for all hosts (all is a automatically created group containing all hosts in the inventory) from the specified inventory file. More on modules in a minute.

If you wish to know more about crating inventories, please refer to How to build an inventory

Setting up ansible.cfg

By default ansible will look for inventory in /etc/ansible/hosts first. To change this behaviour and make our lives easier we will configure ansible to use the Vagrant generated inventory.

Create a file name ansible.cfg in the root of your project and fill it with:

[defaults]
inventory = .vagrant/provisioners/ansible/inventory/vagrant_ansible_inventory
host_key_checking = false

You can now run the command in previous section as:

> ansible all -m debug -a var=inventory_hostname

If you wish to know more about configuring ansible, please refer to Ansible Configuration Settings

Exploring basic playbook structure

Configuration in ansible is done through YAML configuration files. We will explore the YAML syntax largely as we go. However if you wish to know more, please refer to the YAML syntax

Let's dissect the example playbook from Vagrant configuration.

--- # Three dashes signify YAML file, Ansible doesn't care if you forget them though
- name: My first play.
  hosts: all
  tasks:
    - name: "My first task!"
      debug: "msg=Hello from VM - {{ inventory_hostname }}"

- name: My second play!
  hosts: all
  become: True  # get superuser privilages
  tasks:
    - name: Notify user about what I want to do
      debug:
        msg: I'm going to install packages

    # ... tasks for installing a package

    # The `name` field is optional (but improves readability).
    - debug: msg="packages are installed."

Here we can see a playbook with two plays defined:

  • My first play
  • My second play!

The hosts option specifies on which hosts we want to run the play. Here we specify the all group.

The core of a play is the tasks section. In the tasks section we specify a list of tasks we want to execute. Tasks are realized through modules. Here we used the debug module. Modules can take options. We can see the msg option in use here. There are two ways to supply arguments as seen in the example. It doesn't matter which way you choose, just try to be consistent.

The become option allows us to elevate the play to superuser privileges.

If you want to list the options of a module, you can use the ansible-doc command provided with Ansible:

> ansible-doc debug

To run a playbook, use the ansible-playbook command. For example:

> ansible-playbook setup-spark.yml

Installing packages with ansible

Let's start with a clean setup-spark.yml file.

To install a package we will use the apt module. For different distributions there are also modules like dfn or yum and partly distribution agnostic package module (but you still have to account for different package names between distributions).

We will install the ntp daemon for time synchronization.

We add the following to spark-setup.yml.

---
- name: Setup common
  hosts: all
  tasks:
  - name: Install the NTP daemon.
    become: True
    apt:
      name: ntp

Here we can see we can get superuser privileges for a single task only.

After running ansible-playbook setup-spark.yml you should see ansible install the ntp to all hosts.

Enabling a service

To enable a service we use the service module.

To enable and start the ntp service add the following task to the play:

- name: Start ntp service
  service: name=ntp state=started enabled=yes

Note that we could have alternatively used the YAML syntax:

- name: Start ntp service
  service:
    name: ntp
    state: started
    enabled: yes

Installing Apache Spark

Apache Spark is unfortunately not available through the official repositories so we will have to install it manually.

We will assume that ansible has configured one host called master and a group of hosts called workers.

Firstly, we need to install some dependencies, namely Java. We also ensure, that we have python3 installed. We define a new play with this task:

- name: Install spark
  hosts: all
  become: True
  tasks:
  - name: Installing dependencies
    apt:
      name: [ "default-jdk", "python3" ]
      update_cache: True

The update_cache option tells apt to update the local repository cache.

Next, we define a new group and user under which we install the package. We will want to run spark as a service later. For this task, Ansible provides two modules group and user. Creating them is them as straightforward as adding the following tasks:

- name: Create spark group
  group:
    name: spark
    state: present

- name: Create spark non-system user
  user:
    name: spark
    group: spark
    shell: /usr/sbin/nologin

Next, we are going to download the Apache Spark binary. They can be found here: https://downloads.apache.org/spark/. We will be installing spark-3.0.2 with hadoop3.2.

The full link to the corresponding tarball then looks like this:

https://downloads.apache.org/spark/spark-3.0.2/spark-3.0.2-bin-hadoop3.2.tgz

To make the playbook more general we will separate information into variables. Ansible allows us to declare variables quite a few places ( a bit too many for my taste).

We've already defined some variables (host variables in ansible speak) when we configured Vagrant provisioning (spark_ip_address). They live in the inventory.

On a play level we can declare them using the vars option. For the sake of brevity we declared the following variables (which we will use later)

  • spark_mirror: Mirror from which to download Spark (i.e https://downloads.apache.org/spark)

  • spark_version: The version of Spark we wish to use (i.e. "3.0.2")

  • hadoop_version: Version of hadoop. (i.e "hadoop3.2")

  • spark_parent_dir: Location where we wish to put Spark ( i.e. "/usr/local" )

  • spark_link_dir: Directory where will the Spark reside ( i.e. "/usr/local/spark" )

And some variables for convenience:

  • spark_name: Just version with appended spark- prefix ("spark-3.0.2")
  • spark_fullname: Full name of the Spark package. ("{{ spark_name }}-bin-{{ hadoop_version }}")
  • spark_target_dir: Location where we wish to put a specific installation of Spark ( i.e. "/usr/local/spark-3.0.2-bin-hadoop3.2" )
  • spark_tarball: Name of the downloaded tarball. ("{{ spark_fullname }}.tgz")
  • spark_tarball_url: Full link to the package ("{{ spark_mirror }}/{{ spark_name }}/{{ spark_tarball }}")

The playbook with the variables defined will then look like this:

---
- name: Install Apache Spark
  hosts: all
  becme: True
  vars:
    - spark_mirror: "https://downloads.apache.org/spark"
    - spark_version: "3.0.2"
    - hadoop_version: "hadoop3.2"

    - spark_parent_dir: "/usr/local"
    - spark_link_dir: "/usr/local/spark"

    - spark_name: "spark-{{ spark_version }}"
    - spark_fullname: "{{ spark_name }}-bin-{{ hadoop_version }}"
    - spark_target_dir: "{{ spark_parent_dir }}/{{ spark_fullname }}"
    - spark_tarball: "{{ spark_fullname }}.tgz"
    - spark_tarball_url: "{{ spark_mirror }}/{{ spark_name }}/{{ spark_tarball }}"
  tasks:
    # ... tasks

To download the file, Ansible provides a module called get_url. We add the following task:

- name: Downloading Apache Spark sources
  get_url:
    url: "{{ spark_tarball_url }}"
    dest: "/tmp/{{ spark_tarball }}"
    owner: spark
    group: spark
    mode: 0644

Again url, dest, owner, group and mode are relevant options of the module (ansible-doc get-url).

Next, we unpack the archive. We use the unarchive module.

- name: Unpacking tarball
  unarchive:
    remote_src: yes
    dest: "{{ spark_parent_dir }}"
    src: "/tmp/{{ spark_tarball }}"
    owner: spark
    group: spark
    creates: "{{ spark_target_dir }}"

Here we see two notable options. The remote_src informs ansible that the source file is located at the remote machine. Without this option it would try to find the archive on your local host (the machine from which you are running ansible).

The creates option informs ansible about the state of the environment after the task is done. Next time the task is run and the tarball is already unpacked, the task will simply be skipped. Used here, it's actually useless, because the unarchive module is smart enough to infer this without the option. However it can be very useful if you, for example create a file manually through the shell or command module.

Next, we link the module to the desired destination. Note that we could have just renamed the directory, but linking makes it easier when we (potentially) want to manage multiple versions.

- name: Link spark directory
  file:
    src: "{{ spark_parent_dir }}/{{ spark_fullname }}"
    dest: "{{ spark_link_dir }}"
    state: link

Next we have to setup the Spark environment. We want to do two things:

  • Add Spark installation to PATH
  • Setup environment variables for Spark

To add Spark to PATH, we will simply add a new script to /etc/profile.d. These scripts are executed by the shell on startup. To generate the new file we will use a template. Ansible supports the Jinja2 templating engine.

We create a new directory templates/ and add a new file spark.sh.j2 where we export the variables the usual way:

export SPARK_HOME={{ spark_link_dir }}
export PATH="$PATH:{{ spark_target_dir }}/bin:{{ spark_target_dir }}/sbin"

We add the following task to the playbook:

- name: Add spark to environment
  template:
    src: "spark.sh.j2"
    dest: "/etc/profile.d/spark.sh"
    owner: root
    group: root
    mode: 0644

Ansible will automatically substitute the variables using the variables defined in the playbook.

To configure spark environment, we will want to define the following environmental variables:

  • SPARK_MASTER_HOST - IP address of the master
  • SPARK_MASTER_PORT - port on which to connect to master
  • SPARK_LOCAL_IP - IP address on which to start the local Spark process
  • SPARK_HOME - home of the current spark installation
  • PYSPARK_PYTHON - python interpreter to use for PySpark

We will group these into a YAML dictionary, which we put into the vars section.

vars:
    # ... other variables
  - spark_master_ip: "{{ hostvars['master'].spark_ip_address }}"
  - spark_master_port: 7077
    
  - spark_local_ip: "{{ hostvars[inventory_hostname].spark_ip_address }}"
  - spark_worker_port: 7078
    
  - spark_env_vars:
      SPARK_MASTER_HOST: "{{ spark_master_ip }}"
      SPARK_MASTER_PORT: "{{ spark_master_port }}"
      SPARK_LOCAL_IP: "{{ spark_local_ip }}"
      SPARK_HOME: "{{ spark_link_dir }}"
      PYSPARK_PYTHON: "/usr/bin/python3"

We also defined spark_worker_port which we will use later.

Now we create a template to populate the spark-env.sh file found in conf/ directory of the Spark installation.

{% if spark_env_vars is defined %}{% for key, value in spark_env_vars.items() %}
export {{key}}={{value}}
{% endfor %}{% endif %}

Here, we use Jinja in a bit more advanced way, but the result should still be evident.

We add the following task:

- name: Configure spark environment
  template:
    src: "spark-env.sh.j2"
    dest: "{{ spark_target_dir }}/conf/spark-env.sh"
    owner: spark
    group: spark
    mode: 0755

Finally, we cleanup the downloaded files:

- name: Cleanup
  file:
    path: "/tmp/{{ spark_tarball }}"
    state: absent

Adding systemd units

We won't be covering how to define systemd units. If you wish to know more Understanding Systemd Units and Unit Files might be a good start.

We define the following templates:

spark-master.service.j2

[Unit]
Description=Spark Master Service
Wants=network.target network-online.target
After=network.target network-online.target

[Service]
Type=forking
User=spark
WorkingDirectory={{ spark_link_dir }}
ExecStart={{ spark_link_dir }}/sbin/start-master.sh 
ExecStop={{ spark_link_dir }}/sbin/stop-master.sh
Restart=on-abort

[Install]
WantedBy=multi-user.target

spark-worker.service.j2

[Unit]
Description=Spark Worker Service
Wants=network.target network-online.target
After=network.target network-online.target

[Service]
Type=forking
User=spark
WorkingDirectory={{ spark_link_dir }}
ExecStart={{ spark_link_dir }}/sbin/start-slave.sh "spark://{{ spark_master_ip }}:{{ spark_master_port }}" --port {{ spark_worker_port }}
ExecStop={{ spark_link_dir }}/sbin/stop-slave.sh
Restart=on-abort

[Install]
WantedBy=multi-user.target

However, we will want to copy these files to the machines only if systemd is present in the system. That requires some form of flow control. We will use the Ansible when clause.

First, we have to capture the output of a module. In Ansible this is called registering a variable and can be done like this:

- name: Check if systemd exists
  stat: path=/lib/systemd/system/
  register: systemd_check

Here we use the stat module to check the /lib/systemd/system path and register the output as a new variable systemd_check . The contents of this variable are dependent on the module used, so we recommend to use the debug module to check its contents.

We will introduce one more Ansible construct and that is block. It groups multiple tasks together so different options can be applied to them together.

The new tasks together then look like this:

- name: Check if systemd exists
  stat: path=/lib/systemd/system/
  register: systemd_check

- block:
  - name: Create master systemd start script
    template:
      src: "spark-master.service.j2"
      dest: "/etc/systemd/system/spark-master.service"
      owner: root
      group: root
      mode: 0644

  - name: Create worker systemd start script
    template:
      src: "spark-worker.service.j2"
      dest: "/etc/systemd/system/spark-worker.service"
      owner: root
      group: root
      mode: 0644

  when: systemd_check.stat.exists == True
  become: True

Creating roles

We will look at two ways of simplifying playbooks, namely roles and including other YAML files using include.

Roles are usually defined in a roles/ directory and follow a specific directory structure.

To simplify our playbook, we might want to define two roles: - common: role that setups common environment on all host - spark: role that installs Spark

We therefore create the following directory structure:

 roles
 ├── common
 │   └── tasks
 └── spark
     ├── defaults
     ├── tasks
     ├── templates
     └── vars

The individual directories correspond to different parts of playbooks. For complete overview please refer to Role directory structure

Basic overview of the directories:

  • defaults: Contains default variables or variables we expect will be overwritten
  • vars: variables we use within the role
  • tasks: tasks of the role
  • templates: template files

We distribute the configuration from the main playbook into to roles in the following way:

roles/common/tasks/main.yml:

---
- block:
  - name: Install the NTP daemon.
    apt:
      name: ntp

  - name: Start ntp service
    service: name=ntp state=started enabled=yes

  become: True

roles/spark/defaults/main.yml:

---
spark_mirror: "https://downloads.apache.org/spark"
spark_version: "3.0.2"
hadoop_version: "hadoop3.2"

spark_parent_dir: "/usr/local"
spark_link_dir: "/usr/local/spark"

# Custom master configuration
spark_master_ip: "{{ hostvars['master'].ansible_default_ipv4.address
                   | default(hostvars['master'].ansible_all_ipv4_addresses[0]) }}"
spark_master_port: 7077

# IP address Spark binds to on this node
spark_local_ip: "{{ ansible_default_ipv4.address
                  | default(ansible_all_ipv4_addresses[0]) }}"
spark_worker_port: 7078

# Custom spark runtime configuration options
spark_extra_vars: {}

spark_default_vars:
  SPARK_MASTER_HOST: "{{ spark_master_ip }}"
  SPARK_MASTER_PORT: "{{ spark_master_port }}"
  SPARK_LOCAL_IP: "{{ spark_local_ip }}"
  SPARK_HOME: "{{ spark_link_dir }}"

  # Python binary executable to use for PySpark in both driver and workers
  # (default is python2.7 if available, otherwise python). Property
  # spark.pyspark.python take precedence if it is set
  PYSPARK_PYTHON: "/usr/bin/python3"

roles/spark/vars/main.yml:

---
spark_env_vars: "{{ spark_extra_vars | default({}) | combine(spark_default_vars) }}"

spark_name: "spark-{{ spark_version }}"
spark_fullname: "{{ spark_name }}-bin-{{ hadoop_version }}"
spark_tarball: "{{ spark_fullname }}.tgz"
spark_tarball_url: "{{ spark_mirror }}/{{ spark_name }}/{{ spark_tarball }}"
spark_target_dir: "{{ spark_parent_dir }}/{{ spark_fullname }}"

roles/spark/tasks/systemd.yml:

---
- name: Check if systemd exists
  stat: path=/lib/systemd/system/
  register: systemd_check

- block:
  - name: Create master systemd start script
    template:
      src: "spark-master.service.j2"
      dest: "/etc/systemd/system/spark-master.service"
      owner: root
      group: root
      mode: 0644

  - name: Create worker systemd start script
    template:
      src: "spark-worker.service.j2"
      dest: "/etc/systemd/system/spark-worker.service"
      owner: root
      group: root
      mode: 0644

  when: systemd_check.stat.exists == True
  become: True

roles/spark/tasks/main.yml:

- name: Check for existing ansible installation
  stat:
    path: '{{ spark_target_dir }}'
  register: spark_installation
  tags:
    - spark

- name: Download, install and setup Spark environment
  when: not spark_installation.stat.exists
  block:
  - name: Installing dependencies
    apt:
      name: [ "default-jdk", "python3" ]

  - name: Create spark group
    group:
      name: spark
      state: present

  - name: Create spark non-system user
    user:
      name: spark
      group: spark
      shell: /usr/sbin/nologin

  - name: Downloading Apache Spark sources
    get_url:
      url: "{{ spark_tarball_url }}"
      dest: "/tmp/{{ spark_tarball }}"
      owner: spark
      group: spark
      mode: 0644

  - name: Unpacking tarball
    unarchive:
      remote_src: yes
      dest: "{{ spark_parent_dir }}"
      src: "/tmp/{{ spark_tarball }}"
      owner: spark
      group: spark
      creates: "{{ spark_target_dir }}"

  - name: Add spark to environment
    template:
      src: "spark.sh.j2"
      dest: "/etc/profile.d/spark.sh"
      owner: root
      group: root
      mode: 0644

  - name: Configure spark environment
    template:
      src: "spark-env.sh.j2"
      dest: "{{ spark_target_dir }}/conf/spark-env.sh"
      owner: spark
      group: spark
      mode: 0755
  become: True

- name: Link spark directory
  become: True
  file:
    src: "{{ spark_parent_dir }}/{{ spark_fullname }}"
    dest: "{{ spark_link_dir }}"
    state: link

- name: Cleanup
  become: True
  file:
    path: "/tmp/{{ spark_tarball }}"
    state: absent


- name: Include systemd services
  include: systemd.yml

The final directory structure looks like this:

 roles
 ├── common
 │   └── tasks
 │       └── main.yml
 └── spark
     ├── defaults
     │   └── main.yml
     ├── tasks
     │   ├── main.yml
     │   └── systemd.yml
     ├── templates
     │   ├── spark-env.sh.j2
     │   ├── spark-master.service.j2
     │   ├── spark.sh.j2
     │   └── spark-worker.service.j2
     └── vars
         └── main.yml

A few notable changes happened:

  1. default values for spark_master_ip and spark_local_ip have been defined using the Jinja default filter.
  2. definition of spark environmental variables has been moved into spark_default_vars, a new dictionaryspark_extra_vars has been defined and they are combined into the spark_env_vars using the Jinja combine filter
  3. the tasks for systemd are defined in its own file systemd.yml and included from main.yml
  4. the spark installation now proceeds only when it detects that Spark is not installed

Finally, we edit the setup-spark.yml:

- name: Install spark
  hosts: all
  roles:
    - common
    - role: spark
      vars:
        spark_local_ip: "{{ hostvars[inventory_hostname].spark_ip_address }}"
        spark_master_ip: "{{ hostvars['master'].spark_ip_address }}"
  tasks:
    - name: Add vagrant to spark group
      become: True
      user:
        name: vagrant
        groups: spark
        append: yes

- name: Start master node
  hosts: master
  tasks:
    - name: Start master service
      become: True
      service:
        name: spark-master
        state: started
        enabled: yes

    - name: Copy example files to master
      become: True
      copy:
        src: example/
        dest: /example
        owner: spark
        group: spark
        mode: 0755

- name: Start worker nodes
  hosts: all
  tasks:
    - name: Start worker service
      become: True
      service:
        name: spark-worker
        state: started

Some notes to Apache Spark ML

Download the data

Do not forget to distribute the files to the workers!

Boston Housing dataset:

wget https://raw.githubusercontent.com/selva86/datasets/master/BostonHousing.csv

Mnist train and test:

wget https://pjreddie.com/media/files/mnist_train.csv wget https://pjreddie.com/media/files/mnist_test.csv

I have also created a script for downloading the data in pyspark/download_data.sh:

#!/usr/bin/env bash

wget https://raw.githubusercontent.com/selva86/datasets/master/BostonHousing.csv
wget https://pjreddie.com/media/files/mnist_train.csv
wget https://pjreddie.com/media/files/mnist_test.csv

Spark Shell

Find the directory where Spark is installed using echo $SPARK_HOME. In this directory run ./bin/pyspark to enter the Python Spark Shell. This connects you to the cluster automatically by creating SparkSession (more on that later).

Spark Shell is interactive so you can try whatever you want. It's good for learning how Spark ML works.

SparkSession

This is an entry point to the cluster. Every program you want to run on the cluster needs object of this type. Spark Shell creates it without you even noticing.

You can create SparkSession by:

spark = SparkSession.builder.master("spark://192.168.50.10:7077").appName("Linear regression with pipeline - Boston").getOrCreate()

where spark://192.168.50.10:7077 is the address of the master node, then you choose a name for the app and create the SparkSession (or get one earlier created). Note that in older versions there was SparkContext, however the SparkSession replaced it and therefore SparkContext is no longer used.

How to store data?

There are multiple objects that can store data:

  1. RDD - Resilient Distributed Dataset
  2. DataFrame
  3. DataSet

We will talk only about RDD and DataFrames since only these two types we use in our project.

RDD

RDD is the oldest object that represents data. It is

  • immutable - when the object is created it cannot be modified (modification returns a new RDD)
  • fault tolerant - when something goes wrong the app doesn't crash
  • distributed - RDD is divided into logic partitions and distributed between cluster worker nodes and therefore the parallelization is possible
  • lazy evaluated - RDDs are lazy evaluated meaning actions and transformations are evaluated only when necessary. Imagine a person who is really lazy but does everything (you can rely on him). He just postpones all work and when you start to yell that you really need it, he finally does it.

We can perform transformations and actions on RDD:

  • transformations return a new RDD (since it is immutable). Possible transformations are .map(), .filter(), .randomSplit(), ...
  • actions return non-RDD object (for example just an int number) - .first(), .count(), ...

You can create a RDD from existing collections (lists for example) or from files on the disk.

DataFrames

This is the newer object representing data that we will use in our applications.

If you have experience with Pandas DataFames, this is virtually the same. You can think about Spark ML DataFrames as Pandas DataFrames. Spark DataFrames have only some optimizations under the hood.

DataFrame is just a 2D array with labelled columns. It is also:

  • immutable
  • fault tolerant
  • distributed
  • lazy evaluated

You can create one from RDD, existing collections (like lists) or from files on the disk (.csv, .txt, .xml, HDFS, S3, HBase, ...). We create DataFrame in lr_pipeline.py from a .csv file like this:

data = spark.read.format("csv").option('header', 'true').option('inferSchema', 'true').load(filename)

In our video there is explained what all the commands mean.

You can also create DataFrame from a list like this:

our_list = [('Martin', 180), ('David', 182), ('Dennis', 190), ('Tobias', 183)]

columns = ["name", "height"]
our_DataFrame = spark.CreateDataFrame(data=our_list, schema=columns)

Simple operations on DataFrames I didn't have time to show on video

  • df.show(10) ... shows header and first 10 lines of the DataFrame
  • df.printSchema() ... prints schema - the header with column type
  • df.select("col_name").show() ... shows only col_name column
  • df.filter(df["col_name"] > 10).show() .. filters only rows which have a value > 10 in column col_name

And other very useful commands: train, test = df.randomSplit([0.8, 0.2]) ... splits the DataFrame to train and test sets train.schema.names ... returns list of names of the columns

VectorAssembler

Transformer that creates a new column by connecting more columns together to a list. We use it in lr_pipeline.py:

v_assembler = VectorAssembler(inputCols=features_list, outputCol='features')
new_dataframe = v_assembler.transform(old_dataframe)

Pipeline

This is a concept from ML that makes the whole workflow of data easier. You put data into pipeline and the pipeline transforms it to the output. In pipeline there can be many stages - many transformers and estimators. In file lr_pipeline.py we demonstrate a very simple pipeline with just one transformer (polynomial expansion) and one estimator (linear regression):

poly_exp = PolynomialExpansion(degree=3, inputCol="features", outputCol="poly_features")
lr = LinearRegression(regParam=0.1, featuresCol="poly_features")

pipeline = Pipeline(stages=[poly_exp, lr])

Te pipeline then behaves like a simple estimator - you put data to input and on that data you fit a model:

model = pipeline.fit(train)

A model is a transformer. It transforms input data into predictions:

prediction = model.transform(train).select("prediction")

To evaluate our model we can use Evaluators - for linear regression:

evaluator = RegressionEvaluator()

prediction_and_labels = model.transform(train).select("prediction", "label")
print("Precision train: " + str(evaluator.evaluate(prediction_and_labels)))

prediction_and_labels = model.transform(test).select("prediction", "label")
print("Precision test: " + str(evaluator.evaluate(prediction_and_labels)))

The whole file lr_pipeline.py with a prepare_data() function that prepares data for the model looks like this:

from pyspark.ml.linalg import Vectors
from pyspark.ml.feature import VectorAssembler
from pyspark.ml import Pipeline
from pyspark.ml.evaluation import RegressionEvaluator
from pyspark.ml.regression import LinearRegression
from pyspark.ml.feature import PolynomialExpansion
from pyspark.sql import SparkSession

def prepare_data(filename):
    """ 
    Transform data for ML learning algorithm

    Input: Data to be transformed (DataFrame)
    Returns: Transformed data (DataFrame)
    """

    data = spark.read.format("csv").option('header', 'true').option('inferSchema', 'true').load(filename)

    data = data.withColumnRenamed('medv', 'label')
    # get columns that represent features
    features_list = data.columns
    # pop last column since it is our target
    features_list.remove('label')

    # make a new column with a vector of features
    v_assembler = VectorAssembler(inputCols=features_list, outputCol='features')

    return v_assembler.transform(data)

if __name__ == "__main__":
    train_ratio = 0.8
    test_ratio = 1 - train_ratio

    # create SparkSession - the entry to the cluster
    spark = SparkSession.builder.master("spark://192.168.50.10:7077").appName("Linear regression with pipeline - Boston").getOrCreate()

    data = prepare_data("BostonHousing.csv")

    # split data into train and test DataFrames
    train, test = data.randomSplit([train_ratio, test_ratio])

    poly_exp = PolynomialExpansion(degree=3, inputCol="features", outputCol="poly_features")

    lr = LinearRegression(regParam=0.1, featuresCol="poly_features")

    pipeline = Pipeline(stages=[poly_exp, lr])
    # fit the model
    model = pipeline.fit(train)

    evaluator = RegressionEvaluator()

    prediction_and_labels = model.transform(train).select("prediction", "label")
    print("Precision train: " + str(evaluator.evaluate(prediction_and_labels)))

    prediction_and_labels = model.transform(test).select("prediction", "label")
    print("Precision test: " + str(evaluator.evaluate(prediction_and_labels)))

Running the application on the cluster

To run the application on the cluster we use bin/spark-submit script in $SPARK_HOME directory.

Note: every node needs access to the files used in our models. We use Boston Housing and MNIST datasets. I have created a script to download all data. This script has to be run in all worker nodes.

To run the application on our cluster, run: /usr/local/spark/bin/spark-submit --master "spark://192.168.50.10:7077" linear_regression.py 2> logfile

We redirected logs to logfile. If you want to see what Spark is doing, erase 2> logfile.

Note: As you can see in logfile, Spark does many things. It has to initialize the whole cluster, create server where you can watch your jobs (on localhost on port 4040) and many others. Therefore the overhead for our application is large. When we use as little amount of data as in the BostonHousing dataset, the size of the overhead causes the application to run for a longer time than in regular Python. Therefore Spark ML is not suitable for really tiny apps as it takes longer to run them due to the overhead. But Spark ML is excellent when we have large models and large amount of data - the overhead is tiny compared to the model and parallelization is really beneficial.

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