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Installation Guide
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====================
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The latest version of **MDAnalysis** can be installed using :ref:`mamba-installation` (recommended),
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or :ref:`pip-installation`. If you need to install MDAnalysis from source, follow :ref:`source-installation`
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for stable releases. If you are a contributor or developer working on MDAnalysis, follow the
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The latest version of **MDAnalysis** can be installed using :ref:`mamba-installation` (recommended),
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or :ref:`pip-installation`. If you need to install MDAnalysis from source, follow :ref:`source-installation`
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for stable releases. If you are a contributor or developer working on MDAnalysis, follow the
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:ref:`development-installation` for editable installation and code modifications.
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Currently, the :ref:`mamba-installation` installs a version of MDAnalysis that does **not** include `OpenMP`_
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acceleration due to limitations in precompiled conda packages. If you need `OpenMP`_-enabled features,
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consider installing via :ref:`pip-installation` and compiling from source with a compatible compiler and
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Currently, the :ref:`mamba-installation` installs a version of MDAnalysis that does **not** include `OpenMP`_
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acceleration due to limitations in precompiled conda packages. If you need `OpenMP`_-enabled features,
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consider installing via :ref:`pip-installation` and compiling from source with a compatible compiler and
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OpenMP support.
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**MDAnalysisTests** is optional and is a separate :ref:`test suite <mdanalysistests>` used
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for verifying MDAnalysis installations and running User Guide examples. It is not required for
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daily use, but some tutorials rely on it. The package is approximately 90 MB and is not updated frequently.
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**MDAnalysisTests** is optional and is a separate :ref:`test suite <mdanalysistests>` used
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for verifying MDAnalysis installations and running User Guide examples. It is not required for
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daily use, but some tutorials rely on it. The package is approximately 90 MB and is not updated frequently.
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If you plan to use tutorial examples or contribute to MDAnalysis, installing it is recommended.
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MDAnalysis supports specific Python versions. For the latest supported versions, please refer to the
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MDAnalysis supports specific Python versions. For the latest supported versions, please refer to the
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`CHANGELOG`_ or the `PyPI`_. Ensure you have a compatible Python version installed before proceeding.
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.. note::
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MDAnalysis supports **Linux**, **macOS**, and **Windows**.
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MDAnalysis supports **Linux**, **macOS**, and **Windows**.
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- If you encounter errors on **Windows** related to **Microsoft Visual C++ 14.0**, install the required **Build Tools for Visual Studio** from: `Microsoft Visual Studio Downloads`_.
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- If you encounter any other issues following these instructions, seek help on `GitHub Discussions (Installation)`_.
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- If you encounter errors on **Windows** related to **Microsoft Visual C++ 14.0**, install the required **Build Tools for Visual Studio** from: `Microsoft Visual Studio Downloads`_.
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- If you encounter any other issues following these instructions, seek help on `GitHub Discussions (Installation)`_.
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.. _mamba-installation:
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mamba/conda
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mamba/conda
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===========
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For most users, `mamba`_ is the **recommended** way to install MDAnalysis. It is a faster drop-in
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replacement for `conda`_ and efficiently handles dependencies. We also recommend creating a new
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For most users, `mamba`_ is the **recommended** way to install MDAnalysis. It is a faster drop-in
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replacement for `conda`_ and efficiently handles dependencies. We also recommend creating a new
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environment for MDAnalysis to ensure a clean and isolated installation.
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MDAnalysis supports two common ways to install with `mamba`_:
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**1. Recommended: Use Mambaforge**
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`Mambaforge`_ is a minimal `conda`_ distribution that includes `mamba`_ by default, uses the `conda-forge`_ channel
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`Mambaforge`_ is a minimal `conda`_ distribution that includes `mamba`_ by default, uses the `conda-forge`_ channel
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(preferred for MDAnalysis) and avoids clutter from `Anaconda`_ base packages.
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To install MDAnalysis with `Mambaforge`_, follow the `mambaforge installation instructions`_ and then
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.. _pip-installation:
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pip
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pip
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===
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The following command will install or upgrade the latest stable version of MDAnalysis via `pip`_ with core dependencies.
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The following command will install or upgrade the latest stable version of MDAnalysis via `pip`_ with core dependencies.
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This means that some packages required by specific analysis modules will not be installed.
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.. code-block:: bash
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Install from source
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===================
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This section is for **users** who want to install a **specific stable version** of MDAnalysis
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(e.g., for reproducibility or to debug a release). This is **not** intended for development or code contributions.
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This section is for **users** who want to install a **specific stable version** of MDAnalysis
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(e.g., for reproducibility or to debug a release). This is **not** intended for development or code contributions.
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If you're a developer, see :ref:`development-installation`.
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To install from source, you must first ensure that your environment already contains all necessary dependencies.
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To install from source, you must first ensure that your environment already contains all necessary dependencies.
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We recommend you check the :ref:`create-virtual-environment` to set up a clean development environment
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with all required dependencies. We recommend using `mamba`_ or `conda`_ to manage this setup.
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Follow the steps in:
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- `Set up with conda-forge`_
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- `Set up with mamba`_
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- `Set up with mamba`_
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MDAnalysis uses different Git branches for different purposes:
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This section is for **contributors and developers** who want to modify MDAnalysis
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or contribute to its development. You’ll install MDAnalysis in **editable mode**, which allows you to make code changes
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This section is for **contributors and developers** who want to modify MDAnalysis
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or contribute to its development. You’ll install MDAnalysis in **editable mode**, which allows you to make code changes
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without reinstalling the package each time.
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Before installing, follow the steps described in the :ref:`source-installation` to set up a clean environment
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with all dependencies.
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Before installing, follow the steps described in the :ref:`source-installation` to set up a clean environment
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with all dependencies.
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Once your environment is ready, install MDAnalysis in editable mode:
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git checkout -b my-feature-branch # Create a new branch for your changes
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pip install -e package/
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Installing in editable mode (`-e`) means that any changes you make to the MDAnalysis source code are immediately
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Installing in editable mode (`-e`) means that any changes you make to the MDAnalysis source code are immediately
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available without needing to reinstall.
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If you plan to run tests you can install the test suite:
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Use of these flags can give a significant performance boost where the compiler can effectively autovectorise.
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Be sure to use the recommended flags for your target architecture. For example, ARM platforms recommend using ``-mcpu`` instead of ``-march``, while
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Be sure to use the recommended flags for your target architecture. For example, ARM platforms recommend using ``-mcpu`` instead of ``-march``, while
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PowerPC platforms prefer both ``-mcpu`` and ``-mtune``.
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Full discussion of these flags is available elsewhere (such as here in this `wiki`_ or in this `ARM`_ blog post) and a list of supported options should be provided by your compiler. The list for GCC_ is provided here.
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This installation does not download all the datasets; instead, the datasets are cached when they are first downloaded using a Python command.
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