Fed-BioMed software installation

This tutorial gives steps for installing Fed-BioMed components (network, node, researcher) on a single machine. Deployment documentation explains other available setups.

Hardware requirements

• 8GB RAM minimum for handling PyTorch & ML packages

System requirements

Fed-BioMed is developed and tested under up to date version of :

• Linux Ubuntu and Fedora, should also work or be easily ported under most Linux distributions
• MacOS

Check specific guidelines for installation on Windows 11.

Software packages

The following packages are required for Fed-BioMed :

• docker
• docker compose v2: don't confuse it with the obsolete docker-compose v1
• conda
• git

Install docker and docker compose

Linux Fedora

Install and start docker engine packages. In simple cases it is enough to run :

$ sudo dnf install -y dnf-plugins-core
$ sudo dnf config-manager \
    --add-repo \
    https://download.docker.com/linux/fedora/docker-ce.repo
$ sudo dnf install -y docker-ce docker-ce-cli containerd.io
$ sudo systemctl start docker

Allow current account to use docker :

$ sudo usermod -aG docker $USER

Check with the account used to run Fed-BioMed that docker is up and can be used by the current account without error :

$ docker run hello-world

Install docker compose and git :

$ sudo dnf install -y docker-compose-plugin git

MacOS

Install docker and docker compose choosing one of the available options for example :

• official full Docker Desktop installation process, please check product license
• your favorite third party package manager for example :
  • macports provides docker and git ports
  • homebrew provides docker and git formulae
  • don't use the docker-compose v1 from macports or homebrew !
  • for docker compose v2, adapt the manual plugin install procedure by picking the proper binary for your hardware

Check with the account used to run Fed-BioMed docker is up and can be used by the current account without error :

$ docker run hello-world

Other

Connect under an account with administrator privileges, install docker, ensure it is started and give docker privilege for the account used for running Fed-BioMed. Also install docker compose v2 and git

Check with the account used to run Fed-BioMed docker is up and can be used by the current account without error :

$ docker run hello-world

Install conda

Linux Fedora

Simply install the package :

$ sudo dnf install conda

Check conda is properly initialized with the following command that should answer the default (base) environment:

$ conda env list

Other

Install conda package manager.

During the installation process, let the conda installer initialize conda (answer "yes" to “Do you wish the installer to initialize Anaconda3 by running conda init ?”)

Check conda is properly initialized with the following command that should answer the default (base) environment:

$ conda env list

Fed-BioMed software

Download Fed-BioMed software by cloning the git repository :

$ git clone -b master https://github.com/fedbiomed/fedbiomed.git
$ cd fedbiomed

In the following tutorials, Fed-BioMed commands use a path relative to the base directory of the clone, noted as ${FEDBIOMED_DIR}. This is not required for Fed-BioMed to work but enables you to run the tutorials more easily.

The way to setup this directory depends on your operating system (Linux, macOSX, Windows), and on your SHELL.

As an example, on Linux/macOSX with bash/zsh it could be done as:

export FEDBIOMED_DIR=$(pwd)

or

export FEDBIOMED_DIR=${HOME}/where/is/fedbiomed

Remember, that this environment variable must be initialized (to the same value) for all running shells (you may want to declare it in your shell initialization file).

Fed-BioMed is provided under Apache 2.0 License.

We don't provide yet a packaged version of Fed-BioMed (conda, pip).

Conda environments

Fed-BioMed uses conda environments for managing package dependencies.

Create or update the conda environments with :

$ ${FEDBIOMED_DIR}/scripts/configure_conda

List the existing conda environments and check the 3 environments fedbiomed-gui fedbiomed-node fedbiomed-researcher were created :

$ conda env list
[...]
fedbiomed-network        /home/mylogin/.conda/envs/fedbiomed-gui
fedbiomed-node           /home/mylogin/.conda/envs/fedbiomed-node
fedbiomed-researcher     /home/mylogin/.conda/envs/fedbiomed-researcher
[...]

${FEDBIOMED_DIR}/scripts/configure_conda network

${FEDBIOMED_DIR}/scripts/configure_conda node researcher

The Next Step

After the steps above are completed you will be ready to start Fed-BioMed components. In the following tutorial you will learn how to launch components and add data in Fed-BioMed to prepare an experiment.