freva-deployment 2405.1.0

Deployment of the Free Evaluation Framework Freva

Deployment of the Free Evaluation Framework Freva

The code in this repository is used to deploy freva in different computing environments. The general strategy is to split the deployment into 4 different steps, these are :

• Deploy MariaDB service via docker
• Deploy a Hashicorp Vault service for storing and retrieving passwords and other sensitive data via docker (this step get automatically activated once the MariaDB service is set)
• Deploy Databrowser API service via docker
• Deploy command line interface backend (evaluation_system)
• Deploy web front end (freva_web)

Note: A vault server is auto deployed once the mariadb server is deployed. The vault centrally stores all passwords and other sensitive data. During the deployment of the vault server a public key is generated which is used to open the vault. This public key will be saved in the evaluation_system backend root directory. Only if saved this key and the key in the vault match, secrets can be retrieved. Therefore it might be a good idea to deploy, the mariadb server (and with it the vault) and the evaluation_system backend togehter.

On CentOS python SELinux libraries need to be installed. If you choose to install ansible via the install_ansible you'll have to use conda to install libselinux for your CentOS version. For example : conda install -c conda-forge libselinux-cos7-x86_64

Pre-Requisites

The main work will be done by ansible, hence some level of familiarity with ansible is advantageous. Since we are using ansible we can use this deployment routine from a workstation computer (like a Mac-book). You do not need to run the deployment on the machines where things get installed. The only requirement is that you have to setup ansible and you can establish ssh connections to the servers.

Installation on *nix systems or wsl.

If you're using Linux, OsX or a Windows subsystem for Linux (WSL) it should be sufficient to issues the following commands:

python3 pip install -U freva-deployment

This command installs ansible and all required python packages.

Note: On CentOS python SELinux libraries need to be installed. You will need to install libselinux for your CentOS version.

python3 -m pip install libselinux-python3

Using docker

A pre-build docker image is available to run the deployment

docker run -it -v /path/to/config:/opt/freva-deployment:z ghcr.io/freva-clint/freva-deployment

The -it flags are important in order to interact with the program. To use and save existing configurations you can mount the directories of the config files into the container.

Commands after installation:

The pip install command will create four different commands:

• deploy-freva-map: To setup a service that keeps track of all deployed freva instances and their services.
• deploy-freva: Text user interface to configure and run the deployment.
• deploy-freva-cmd: Run already configured deployment.
• freva-service: Start|Stop|Restart|Check services of freva instances.
• freva-migrate: Command line interface to manage project migration from old freva systems to new ones. If you can't find the commands mentioned above pip was probably installing them in the user space. In that case you need to append your PATH environment variable by ~/.local/bin.If you use bash for example, add the following command to your local .bashrc:

export PATH=$PATH:$HOME/.local/bin

Installing docker-compose/podman-compose and sudo access to the service servers

Because the services of MariaDB, DatabrowserAPI and Apache httpd will be deployed on docker container images, docker needs to be available on the target servers. Since version v2309.0.0 of the deployment the containers are set up using doker-compose. Hence docker-compose (or podman-compose) has to be installed on the host systems. Usually installing and running docker requires root privileges. Hence, on the servers that will be running docker you will need root access. There exists an option to install and run docker without root, information on a root-less docker option can be found on the docker docs

Note: Some systems use podman instead of docker. The deployment routine is able to distinguish and use the right service.

Configuring the deployment

A complete freva instance will need the following services:

• solrservers (hostname of the apache solr server)
• dbservers (hostname of the MariaDB server)
• webservers (hostname that will host the web site)
• backendservers (hostname(s) where the command line interface will be installed)

Two typical server topography could look the following:

Two different server structures. In setup I the services are running on the same host that serve 4 docker containers. The backend is installed on a hpc login node with access to a gpfs/lustre file system. Setup II deploys the MariaDB, Solr services and the website on dedicated servers. The command line interfaces are also deployed on independent servers.

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Setting the python and git path

Some systems do not have access to python3.6+ (/usr/bin/python3) or git by default. In such cases you can overwrite the ansible_python_interpreter in the inventory settings of the server section to point ansible to a custom python3 bindary. For example

ansible_python_interpreter=/sw/spack-rhel6/miniforge3-4.9.2-3-Linux-x86_64-pwdbqi/bin/python3

The same applies to the path to the git binary:

git_path=/sw/spack-levante/git-2.31.1-25ve7r/bin/git

Running the deployment

After successful configuration you can run the deployment. The command deploy-freva opens a text user interface (tui) that will walk you through the setup of the deployment. The tui allows to edit, save, load and run a configuration file

Note: Navigation is similar to the one of the nano text editor. The shortcuts start with a ^ which indicates CTRL+.

• the pop up menus (e.g. Exit) must be navigated pressing tab to select the options and then Enter.
• the configuration files must be saved as a .toml as the the tui only recognises this extension.
• to paste with the mouse (*nix style), double middle click.

Unique identifiers via a domain flag

Different freva instances are installed across different institutions. Usually the different freva instances running at an institution are distinguished by a unique project name associated with each freva instance for example xces. To make the project names unique across institutions (domains) a domain flag should be set for the deployment. For example all freva instances running at the German Climate Computing Centre will get the dkrz domain flag while freva instances running at Free Uni Berlin get the fub domain flag. This allows for easy identification of the right freva instance for remote servicing. Please remember to set the correct domain flag for deployment, servicing and migration of an old freva system.

Deployment with existing configuration.

If you already have a configuration saved in a toml base inventory file you can issue the deploy-freva-cmd command:

eploy-freva-cmd --help
usage: deploy-freva-cmd [-h] [--config CONFIG] [--steps {web,core,db,databrowser} [{web,core,db,databrowser} ...]] [--ask-pass] [--ssh-port SSH_PORT] [-v] [-l]
                        [--gen-keys] [-V]

Deploy freva and its services on different machines.

options:
  -h, --help            show this help message and exit
  --config CONFIG, -c CONFIG
                        Path to ansible inventory file. (default: /home/wilfred/.anaconda3/share/freva/deployment/inventory.toml)
  --steps {web,core,db,databrowser} [{web,core,db,databrowser} ...]
                        The services/code stack to be deployed (default: ['db', 'databrowser', 'web', 'core'])
  --ask-pass            Connect to server via ssh passwd instead of public key. (default: False)
  --ssh-port SSH_PORT   Set the ssh port, in 99.9% of the cases this should be 22 (default: 22)
  -v, --verbose         Verbosity level (default: 0)
  -l, --local           Deploy services on the local machine, debug purpose. (default: False)
  --gen-keys            Generate public and private web certs, use with caution. (default: False)
  -V, --version         show program's version number and exit

The --steps flags can be used if not all services should be deployed.

Kown Issues:

Below are possible solutions to some known issues:

SSH connection fails:

fatal: [host.name]: FAILED! => {"msg": "Using a SSH password instead of a key is not possible because Host Key checking is enabled and sshpass does not support this.  Please add this host's fingerprint to your known_hosts file to manage this host."}

• This means that you've never logged on to the server. You can avoid this error message by simply logging on to the server for the first time.

Playbook complains about refused connections for the solr or db playbook

fatal: [localhost]: FAILED! => {"changed": true, "cmd": "docker run --name \"test_ces_db\" -e MYSQL_ROOT_PASSWORD=\"T3st\" -p \"3306\":3306 -d docker.io/library/mariadb", "delta": "0:00:00.229695", "end": "2021-05-27 16:10:58.553280", "msg": "non-zero return code", "rc": 125, "start": "2021-05-27 16:10:58.323585", "stderr": "docker: Error response from daemon: driver failed programming external connectivity on endpoint test_ces_db (d106bf1fe310a2ae0e012685df5a897874c61870c5241f7a2af2c4ce461794c2): Error starting userland proxy: listen tcp4 0.0.0.0:3306: bind: address already in use.", "stderr_lines": ["docker: Error response from daemon: driver failed programming external connectivity on endpoint test_ces_db (d106bf1fe310a2ae0e012685df5a897874c61870c5241f7a2af2c4ce461794c2): Error starting userland proxy: listen tcp4 0.0.0.0:3306: bind: address already in use."], "stdout": "895ba35cdf5dcf2d4ec86997aedf0637bf4020f2e9d3e5775221966dcfb820a5", "stdout_lines": ["895ba35cdf5dcf2d4ec86997aedf0637bf4020f2e9d3e5775221966dcfb820a5"]}

• This means that there is already a service running on this port - in this case a local mariadb service. To avoid this error chose a different port in your config/inventory file.

Playbook cannot create database tables because connections fails

fatal: [localhost]: FAILED! => {"changed": false, "msg": "ERROR 1698 (28000): Access denied for user 'root'@'localhost'\n"}

• This is a common problem if you've set the mariadb docker host to be localhost. You can avoid the problem by setting the db_host variable to a non localhost type IP like 172.17.0.1. If you're not sure what IP to use try the following command

docker inspect -f '{{range .NetworkSettings.Networks}}{{.IPAddress}}{{end}}' db_docker_name

you can figure out the db_docker_name using the following command:

docker container ls

Git related unit tests in core playbook fail

Git pull and push commands tend to fail if you haven't configured git. In this case change into the /tmp/evaluation_system directory of the host that runs the playbook then manually trigger the unit tests by

FREVA_ENV=/path/to/root_dir make tests

You can then check the stderr for messages for git related issues. Usually it helps to configure git before hand:

git config --global init.defaultBranch main
git config --global user.name your_user
git config --global user.email [e-mail]

Advanced: Adjusting the playbook

Playbook templates and be found the in the playbooks directory. You can also add new variables to the playbook if they are present in the config/inventory file.

Contributing to freva-deployment

We welcome contributions from the community! Before you start contributing, please follow these steps to set up your development environment. Make sure you have the following prerequisites installed:

• Python (>=3.x)
• Git
• Make

git clone https://github.com/FREVA-CLINT/freva-deployment.git
cd freva-deployment.git
make

The deployment routine is supposed to interact with the user - this can can be asking for user names or passwords. To avoid such interaction you can set the following environment variables.

• MASTER_PASSWD: the admin/root password for all services (db, web etc).
• EMAIL_USER: the user name for email server login credentials.
• EMAIL_PASSWD: the password for email server login credentials.
• ANSIBLE_BECOME_PASSWORD: the password used in any sudo command.

These environment variables have only an effect when the deployment is applied in debug or local mode using the -l flag.

Using a local VM for testing.

A test freva instance can be deployed on a dedicated local virtual machine. This virtual machine is based on a minimal ubuntu server image and has docker and podman pre installed. To create the virtual machine simply run the following script.

cloud-init/start-vm.sh -h

Usage: start-vm.sh [-k|--kill], [-p|--port PORT]
Create a new virtual machine (VM) ready for freva deployment.
Options:
  -k, --kill     Kill the virtual machine
  -p, --port     Set the port of the service that is used to configure the VM default: 8000

Note: Before running the script you will have to install qemu. The script has only been tested on Linux systems.

You can then make use of the pre configured inventory file in assets/share/freva/deployment/config/inventory.toml. In order to deploy freva on the newly created VM you will have to instruct ansible to use ssh port 2222 instead of 22.

The following command will install freva along all with it's components to the local VM:

deploy-freva-cmd  assets/share/freva/deployment/config/inventory.toml --gen-keys --ssh-port 2222

If you want to tear down the created VM you can either press CTRL+C in the terminal where you created the VM or use the kill command:

./cloud-init/start-vm.sh -k

Development Workflow

To install the code in development mode use:

make

Unit tests, building the documentation, type annotations and code style tests are done with tox. To run all tests, linting in parallel simply execute the following command:

tox -p 3

You can also run the each part alone, for example to only check the code style:

tox -e lint

available options are lint, types, test and docs.

Tox runs in a separate python environment to run the tests in the current environment use:

pytest

To reformat and do type checking:

make lint

Creating a new release.

Once the development is finished and you decide that it's time for a new release of the software use the following command to trigger a release procedure:

tox -e release

This will check the current version of the main branch and trigger a GitHub continuous integration pipeline to create a new release. The procedure performs a couple of checks, if theses checks fail please make sure to address the issues.