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Python bundles

Introduction

  • The bundle names reflect the content, like Python packages, and its version, but also which Python version, compilers and libraries that are compatible with it.

  • The module endings may contain GCCcore-X.Y.Z and/or [YEAR-a/b]. Example SciPy-bundle/2024.05-gfbf-2024a or Python/3.12.3-GCCcore-13.3.0

    • GCCcore reflects the GCC compiler version that is compatible when using C/C++ "back end" code.
    • The year reflects an EasyBuild toolchain, see FOSS toolchains.

FOSS tool chains and Python version using them

FOSS Python version
2023b 3.11.5
2024a 3.12.3
2025a 3.13.1
  • foss is the full level toolchain.
  • gfbf means that the libraries FlexiBLAS (incl. LAPACK) + FFTW are included.

  • gompi means that the MPI library OpenMPI is included.

  • See Toolchain diagram

Warning

  • Make sure to use bundles that are compatible with each-other and with needed Python version.
  • Otherwise it is better to create isolated environments with Conda or virtual environments, see Virtual environments in Python.

Biopython

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

Main package(s)

  • biopython

Installed versions

Versions and dependencies

1.84-foss-2024a

Some dependencies

  • Python/3.12.3-GCCcore-13.3.0
  • SciPy-bundle/2024.05-gfbf-2024a
  • Python-bundle-PyPI/2024.06-GCCcore-13.3.0

IPython

IPython provides a rich architecture for interactive computing with:

  • Powerful interactive shells (terminal and Qt-based).
  • A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media.
  • Support for interactive data visualization and use of GUI toolkits.
  • Flexible, embeddable interpreters to load into your own projects.
  • Easy to use, high performance tools for parallel computing.

Main package(s)

  • ipython
  • matplotlib-inline

Installed versions

Versions and dependencies

8.28.0-GCCcore-13.3.0

Dependencies

  • Python/3.12.3-GCCcore-13.3.0
  • Python-bundle-PyPI/2024.06-GCCcore-13.3.0

JupyterLab

JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook.

Main package(s)

  • jupyterlab

Installed versions

Versions and dependencies

4.2.5-GCCcore-13.3.0
  • Python/3.12.3-GCCcore-13.3.0
  • Python-bundle-PyPI/2024.06-GCCcore-13.3.0
  • IPython/8.28.0-GCCcore-13.3.0

matplotlib

matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms.

matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.

Main package(s)

  • contourpy
  • Cycler
  • fonttools
  • kiwisolver
  • matplotlib

Load this version and get many other bundles on the fly!

Included are

  • Python-bundle-PyPI/2024.06-GCCcore-13.3.0
  • SciPy-bundle/2024.05-gfbf-2024a

Installed versions

Versions and dependencies

3.9.2-gfbf-2024a

Packages

  • contourpy-1.3.0
  • Cycler-0.12.1
  • fonttools-4.53.1
  • kiwisolver-1.4.5
  • matplotlib-3.9.2

Dependencies

  • Python/3.12.3-GCCcore-13.3.0
  • Python-bundle-PyPI/2024.06-GCCcore-13.3.0
  • SciPy-bundle/2024.05-gfbf-2024a

mpi4py

MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.

Main package(s)

  • mpi4py

Installed versions

Versions and dependencies

3.1.5-gompi-2023b
  • Python/3.11.5-GCCcore-13.2.0
  • OpenMPI/4.1.6-GCC-13.2.0
4.0.1-gompi-2024a
  • Python/3.12.3-GCCcore-13.3.0
  • OpenMPI/5.0.3-GCC-13.3.0

numba

Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.

Main package(s)

  • numba
  • llvmlite

Are you on a GPU node?

  • Load a CUDA module and numba will use the GPU!

Installed versions

Versions and dependencies

numba/0.60.0-foss-2024a

Packages

  • llvmlite-0.43.0

Dependencies

  • Python/3.12.3-GCCcore-13.3.0
  • Python-bundle-PyPI/2024.06-GCCcore-13.3.0
  • SciPy-bundle/2024.05-gfbf-2024a

Python-bundle-PyPI

Bundle of Python packages from PyPI

Main package(s)

  • Type ml help Python-bundle-PyPI/[version] on Pelle to see an output.

Among others:

  • chardet
  • future
  • Jinja
  • pkginfo
  • psutil
  • Pygments
  • pydevtool
  • pytest
  • pytz
  • regex
  • Sphinx
  • threadpoolctl
  • toml
  • urllib

Also loads the package module

  • virtualenv

Installed versions

Versions and dependencies

2023.06-GCCcore-12.3.0
  • Python/3.11.5-GCCcore-13.2.0
2023.10-GCCcore-13.2.0
  • Python/3.11.5-GCCcore-13.2.0
2023.10-GCCcore-13.3.0
  • Python/3.11.5-GCCcore-13.3.0
2024.06-GCCcore-13.3.0
  • Python/3.12.3-GCCcore-13.3.0
2025.04-GCCcore-14.2.0
  • Python/3.13.1-GCCcore-14.2.0

PyTorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.

Main package(s)

  • torch

Installed versions

Versions and dependencies

2.6.0-foss-2024a
  • Python/3.12.3-GCCcore-13.3.0
  • OpenMPI/5.0.3-GCC-13.3.0

scikit-learn

Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.

Main package(s)

  • scikit-learn (sklearn as alias)

Installed versions

Versions and dependencies

1.6.1-gfbf-2024a

Packages

  • scikit-learn-1.6.1

Dependencies

  • Python/3.12.3-GCCcore-13.3.0
  • Python-bundle-PyPI/2024.06-GCCcore-13.3.0
  • SciPy-bundle/2024.05-gfbf-2024a

SciPy-bundle

Bundle of Python packages for scientific software

Main package(s)

  • numpy
  • pandas
  • scipy

Installed versions

Versions and dependencies

2023.07-gfbf-2023a

Packages

  • numpy-1.25.1
  • pandas-2.0.3
  • scipy-1.11.1

Dependencies

  • Python/3.11.3-GCCcore-12.3.0
  • Python-bundle-PyPI/2023.06-GCCcore-12.3.0
2023.11-gfbf-2023b

Packages

  • numpy-1.26.2
  • pandas-2.1.3
  • scipy-1.11.4

Dependencies

  • Python/3.11.5-GCCcore-13.2.0
  • Python-bundle-PyPI/2023.10-GCCcore-13.2.0
2024.05-gfbf-2024a

Packages

  • numpy-1.26.4
  • pandas-2.2.2
  • scipy-1.13.1

Dependencies

  • Python/3.12.3-GCCcore-13.3.0
  • Python-bundle-PyPI/2024.06-GCCcore-13.3.0

sympy

SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.

Main package(s)

  • sympy

Installed versions

Versions and dependencies

1.13.3-gfbf-2024a
  • Python/3.12.3-GCCcore-13.3.0
  • Python-bundle-PyPI/2024.06-GCCcore-13.3.0
  • SciPy-bundle/2024.05-gfbf-2024a

xarray

xarray (formerly xray) is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures.

Main package(s)

  • xarray

Installed versions

Versions and dependencies

2024.11.0-gfbf-2024a
  • Python/3.12.3-GCCcore-13.3.0
  • Python-bundle-PyPI/2024.06-GCCcore-13.3.0
  • SciPy-bundle/2024.05-gfbf-2024a