Installation

Prerequisites

• shell (bash, csh, etc, if running on Windows, use a linux container)
• python3 >= python3.8
• pip3
• wget
• build tools (make, C/C++ compiler)
• (OPTIONAL) docker (required for 4. Run a Real Simulation)
• (OPTIONAL) file editor for docker config file editing

Estimated Time

20 minutes

You Will Learn

• How to install Merlin in a virtual environment using pip.
• How to install a container platform eg. Singularity, Docker, or Podman.
• How to configure Merlin.
• How to test/verify the installation.

This section details the steps necessary to install Merlin and its dependencies. Merlin will then be configured for the local machine and the configuration will be checked to ensure a proper installation.

Installing Merlin

A Merlin installation is required for the subsequent modules of this tutorial.

Once Merlin is installed, it requires servers to operate. While you are able to host your own servers, we will use Merlin's containerized servers in this tutorial. However, if you prefer to host your own servers you can host a Redis server that is accessible to your current machine. Your computer/organization may already have a Redis server available you can use, please check with your local system administrator.

Create a virtualenv using python3 to install Merlin.

python3 -m venv --prompt merlin merlin_venv

Activate the virtualenv.

bashcsh

source merlin_venv/bin/activate

source merlin_venv/bin/activate.csh

The (merlin) <shell prompt> will appear after activating.

You should upgrade pip and setuptools before proceeding.

pip3 install setuptools pip -U

Install Merlin through pip.

Latest VersionSpecific Version

pip3 install merlin

pip3 install merlin==x.y.z

Check to make sure Merlin installed correctly.

which merlin

You should see that it was installed in your virtualenv, like so:

Success

<path_to_virtualenv>/merlin_venv/bin/merlin

If this is not the output you see, you may need to restart your virtualenv and try again.

You'll need the virtualenv activated for the subsequent steps in the tutorial. Once you've finished you can deactivate the virtual environment with:

deactivate

Redis Server

A Redis server is required for the Celery results backend server, this same server can also be used for the Celery broker. We will be using Merlin's containerized server however we will need to download one of the supported container platforms avaliable. For the purpose of this tutorial we will be using Singularity.

Installing Singularity

Update and install Singularity dependencies:

apt-get update && apt-get install -y build-essential libssl-dev uuid-dev libgpgme11-dev squashfs-tools libseccomp-dev pkg-config

Download dependency go:

wget https://go.dev/dl/go1.18.1.linux-amd64.tar.gz

Extract go into local:

tar -C /usr/local -xzf go1.18.1.linux-amd64.tar.gz

Remove go tar file:

rm go1.18.1.linux-amd64.tar.gz

Update PATH to include go:

export PATH=$PATH:/usr/local/go/bin

Download Singularity:

wget https://github.com/sylabs/singularity/releases/download/v3.9.9/singularity-ce-3.9.9.tar.gz

Extract Singularity:

tar -xzf singularity-ce-3.9.9.tar.gz

Configure and Install Singularity:

cd singularity-ce-3.9.9 ./mconfig && make -C ./builddir && sudo make -C ./builddir install

Configuring Merlin

Merlin requires a configuration script for the Celery interface in order to know which server(s) to connect to. Run this configuration method to create the app.yaml configuration file.

merlin config --broker redis

The merlin config command above will create a file called app.yaml in the ~/.merlin directory. If you are running a Redis server locally then you are all set, look in the ~/.merlin/app.yaml file to see the configuration, it should look like the configuration below.

app.yaml

broker:
  name: redis
  server: localhost
  port: 6379
  db_num: 0

results_backend:
  name: redis
  server: localhost
  port: 6379
  db_num: 0

More detailed information on configuring Merlin can be found in the Configuration page.

Checking/Verifying Installation

First launch the Merlin server containers by using the merlin server commands.

Initialize the server files:

merlin server init

This will create a merlin_server/ folder in the current run directory. The structure of this folder will look like so:

merlin_server/
|-- redis.conf
|-- redis.pass
|-- redis.users
`-- redis_latest.sif

The files in this folder are:

1. redis.conf: The Redis configuration file that contains all of the settings to be used for our Redis server
2. redis.pass: A password for the Redis server that we'll start up next
3. redis.users: A file defining the users that are allowed to access the Redis server and their permissions
4. redis_latest.sif: A singularity file that contains the latest Redis docker image that was pulled behind the scenes by Merlin

If you'd like to modify the configuration of your server, you can either modify the files directly or use:

merlin server config

Now that we have the necessary server files initialized, start the server:

merlin server start

With this command, the containerized server should now be started. Notice that two new files were added to the merlin_server folder:

1. merlin_server.pf: A process file containing information regarding the Redis process
2. app.yaml: A new app.yaml file configured specifically for the containerized Redis server that we just started

To have Merlin read this configuration, copy it to your current run directory:

cp merlin_server/app.yaml .

You can also make this server container your main server configuration by replacing the one located in your home directory. Make sure you make back-ups of your current app.yaml file in case you want to use your previous configurations.

mv ~/.merlin/app.yaml ~/.merlin/app.yaml.bak

cp ./merlin_server/app.yaml ~/.merlin/

Note

Since Merlin servers are created locally on your run directory you are allowed to create multiple instances of Merlin server with their unique configurations for different studies. Simply create different directories for each study and run the following command in each directory to create an instance for each:

merlin server init

The merlin info command will check that the configuration file is installed correctly, display the server configuration strings, and check server access.

merlin info

If everything is set up correctly, you should see:

Expected Output for Successful Config

       *      
   *~~~~~                                       
  *~~*~~~*      __  __           _ _       
 /   ~~~~~     |  \/  |         | (_)      
     ~~~~~     | \  / | ___ _ __| |_ _ __  
    ~~~~~*     | |\/| |/ _ \ '__| | | '_ \ 
   *~~~~~~~    | |  | |  __/ |  | | | | | |
  ~~~~~~~~~~   |_|  |_|\___|_|  |_|_|_| |_|
 *~~~~~~~~~~~                                    
   ~~~*~~~*    Machine Learning for HPC Workflows                                 



Merlin Configuration
-------------------------

config_file        | /path/to/app.yaml
is_debug           | False
merlin_home        | /path/to/.merlin
merlin_home_exists | True
broker server      | redis://default:******@127.0.0.1:6379/0
broker ssl         | False
results server     | redis://default:******@127.0.0.1:6379/0
results ssl        | False

Checking server connections:
----------------------------
broker server connection: OK
results server connection: OK

Python Configuration
-------------------------

$ which python3
/path/to/python3

$ python3 --version
Python x.y.z

$ which pip3
/path/to/pip3

$ pip3 --version
pip x.y.x from /path/to/pip (python x.y)

"echo $PYTHONPATH"

Docker Advanced Installation (Optional)

This optional section details the setup of a RabbitMQ server and a Redis TLS (Transport Layer Security) server for Merlin. For this section, we'll start with the following docker-compose.yml file:

Initial Docker Compose

docker-compose.yml

version: '3'

networks:
  mernet:
    driver: bridge

services:
  redis:
    image: 'redis:latest'
    container_name: my-redis
    ports:
      - "6379:6379"
    networks:
      - mernet

  merlin:
    image: 'llnl/merlin'
    container_name: my-merlin
    tty: true
    volumes:
      - ~/merlinu/:/home/merlinu
    networks:
      - mernet

RabbitMQ Server

A RabbitMQ server can be started to provide the broker, the Redis server will still be required for the backend. Merlin is configured to use ssl encryption for all communication with the RabbitMQ server. An ssl server requires ssl certificates to encrypt the communication through the python ssl module python ssl. This tutorial can use self-signed certificates created by the user for use in the RabbitMQ server. The RabbitMQ server uses TLS (often known as "Secure Sockets Layer"). Information on RabbitMQ with TLS can be found here: RabbitMQ TLS.

A set of self-signed keys is created through the tls-gen package. These keys are then copied to a common directory for use in the RabbitMQ server and python.

git clone https://github.com/michaelklishin/tls-gen.git
cd tls-gen/basic
make CN=my-rabbit CLIENT_ALT_NAME=my-rabbit SERVER_ALT_NAME=my-rabbit
make verify
mkdir -p ${HOME}/merlinu/cert_rabbitmq
cp result/* ${HOME}/merlinu/cert_rabbitmq

The RabbitMQ docker service can be added to the previous docker-compose.yml file:

RabbitMQ Docker Compose

docker-compose.yml

version: '3'

networks:
mernet:
driver: bridge

services:
redis:
image: 'redis:latest'
container_name: my-redis
ports:
  - "6379:6379"
networks:
  - mernet

rabbitmq:
image: rabbitmq:3-management
container_name: my-rabbit
tty: true
ports:
  - "15672:15672"
  - "15671:15671"
  - "5672:5672"
  - "5671:5671"
environment:
  - RABBITMQ_SSL_CACERTFILE=/cert_rabbitmq/ca_certificate.pem
  - RABBITMQ_SSL_KEYFILE=/cert_rabbitmq/server_key.pem
  - RABBITMQ_SSL_CERTFILE=/cert_rabbitmq/server_certificate.pem
  - RABBITMQ_SSL_VERIFY=verify_none
  - RABBITMQ_SSL_FAIL_IF_NO_PEER_CERT=false
  - RABBITMQ_DEFAULT_USER=merlinu
  - RABBITMQ_DEFAULT_VHOST=/merlinu
  - RABBITMQ_DEFAULT_PASS=guest
volumes:
  - ~/merlinu/cert_rabbitmq:/cert_rabbitmq
networks:
  - mernet

merlin:
image: 'llnl/merlin'
container_name: my-merlin
tty: true
volumes:
  - ~/merlinu/:/home/merlinu
networks:
  - mernet

When running the RabbitMQ broker server, the config can be created with the default merlin config command. If you have already run the previous command then remove the ~/.merlin/app.yaml or ~/merlinu/.merlin/app.yaml file , and run the merlin config command again.

merlin config

The app.yaml file will need to be edited to add the RabbitMQ settings in the broker section of the app.yaml file. The server: should be changed to my-rabbit. The RabbitMQ server will be accessed on the default TLS port, 5671.

RabbitMQ app.yaml

app.yaml

broker:
  name: rabbitmq
  server: my-rabbit
  password: ~/.merlin/rabbit.pass

results_backend:
  name: redis
  server: my-redis
  port: 6379
  db_num: 0

To complete the config create a password file:

touch ~/merlinu/.merlin/rabbit.pass

Then open the file and add the password guest.

The aliases defined previously can be used with this set of docker containers.

Redis TLS Server

This optional section details the setup of a Redis server with TLS for Merlin. The Redis TLS configuration can be found in the Security With Redis section. A newer Redis (version 6 or greater) must be used to enable TLS.

A set of self-signed keys is created through the tls-gen package. These keys are then copied to a common directory for use in the Redis server and python.

git clone https://github.com/michaelklishin/tls-gen.git
cd tls-gen/basic
make CN=my-redis CLIENT_ALT_NAME=my-redis SERVER_ALT_NAME=my-redis
make verify
mkdir -p ${HOME}/merlinu/cert_redis
cp result/* ${HOME}/merlinu/cert_redis

The configuration below does not use client verification --tls-auth-clients no so the ssl files do not need to be defined as shown in the Security With Redis section.

RabbitMQ & Redis TLS Docker Compose

docker-compose.yml

version: '3'

networks:
  mernet:
    driver: bridge

services:
  redis:
    image: 'redis'
    container_name: my-redis
    command:
      - --port 0
      - --tls-port 6379
      - --tls-ca-cert-file /cert_redis/ca_certificate.pem
      - --tls-key-file /cert_redis/server_key.pem
      - --tls-cert-file /cert_redis/server_certificate.pem
      - --tls-auth-clients no
    ports:
      - "6379:6379"
    volumes:
      - "~/merlinu/cert_redis:/cert_redis"
    networks:
      - mernet

  rabbitmq:
    image: rabbitmq:3-management
    container_name: my-rabbit
    tty: true
    ports:
      - "15672:15672"
      - "15671:15671"
      - "5672:5672"
      - "5671:5671"
    volumes:
      - "~/merlinu/rabbbitmq.conf:/etc/rabbitmq/rabbitmq.conf"
      - "~/merlinu/cert_rabbitmq:/cert_rambbitmq"
    networks:
      - mernet

The rabbitmq.conf file contains the configuration, including ssl, for the RabbitMQ server.

RabbitMQ Config with SSL

rabbitmq.conf

default_vhost = /merlinu
default_user = merlinu
default_pass = guest
listeners.ssl.default = 5671
ssl.options.ccertfile = /cert_rabbitmq/ca_certificate.pem
ssl.options.certfile = /cert_rabbitmq/server_certificate.pem
ssl.options.keyfile = /cert_rabbitmq/server_key.pem
ssl.options.verify = verify_none
ssl.options.fail_if_no_peer_cert = false

Once this docker-compose file is run, the Merlin app.yaml file is changed to use the Redis TLS server rediss instead of redis.