Troubleshooting and FAQ

This page contains some frequently encountered problems, and their solutions.

Missing Python interpreter in Jupyter notebook

If Fed-BioMed is installed in a virtual environment such as virtualenv or conda, executing fedbiomed researcher -p <component-dir> may not use the correct Python interpreter. This issue can be resolved by installing the necessary packages for the virtual environment tool, either automatically or by manually registering a Python kernel.

For Conda users, installing nb_conda_kernels will automatically detect the Python interpreters from created virtual environments and allow you to select them.

For other tools, you may need to install ipykernel and register the Python interpreter manually. After activating your virtual environment, execute the following command:

python -m ipykernel install --user --name=<project-kernel-name>

Another option is to add the Python path to the PATH variable:

export PATH=<path/to/python3>:$PATH

Tkinter Error on macOS or Missing python-tk Package

Fed-BioMed uses the itk module in its CLI to launch a file explorer for selecting files and folders. However, some systems or Python environment managers may not include python-tk, which can cause failures—for example, when adding datasets into nodes via the Fed-BioMed CLI. If you're using tools like pyenv to install different Python versions without python-tk being present on your system, this will result in a Python installation without the correct tk module.

You can verify if itk or python-tk is correctly installed by running the following test code:

import tkinter
tkinter._test()

If the necessary modules are not installed, you may encounter an exit error on macOS similar to this:

macOS 14 (1407) or later required, have instead 14 (1406)!

If this occurs, you can install python-tk by running brew install python-tk

After installing, reinstall the Python version using pyenv to ensure the correct setup.

This issue may also occur if you're using a conda virtual environment. To ensure tk is correctly installed in conda, run:

conda install -c conda-forge tk

Tkinter error on Linux

Similar to macOS, on Linux you may encounter errors due to the lack of the tkinter module installed on your local machine. On Linux systems, please run sudo apt-get install python3-tk before creating a pyenv for a specific Python version, or before using any other virtual environment tool.

On Fedora, please use sudo dnf install tk-devel.

Missing gmp.h, mpfr.h and mpc.h

Some Fed-BioMed secure aggregation modules uses gmpy2 for big integer operation. This module requires to have libgmp3-dev and libmpfr-dev and libmpc-dev installed on Linux debian distributions (and equivalents on different Linux distributions). In case of missing gmp.h, mpfr.h, or mpc.h module errors please install apt-get install libgmp3-dev libmpfr-dev libmpc-dev.

On maxOs please install: brew link gmp mpfr mpc.