Installing from source

MDAnalysis is open source and you can always build and install the package from source. This gives you the flexibility to use either the latest releases or, if you like living on the cutting edge, you can also use the current development version of the code. This page contains notes on how to install from source.

For alternative ways to install MDAnalysis, see the page Install.

Installing from source

MDAnalysis is also distributed in source form. In order to build the library some C code needs to be compiled. Thus you will need

• python (>=2.7 or >=3.4)
• a C compiler (GNU gcc works), Microsoft Visual C++ 14.0 on Windows
• the Python header files (typically in a package python-dev),
• numpy and cython

See Additional non-standard packages below for what else you need at run time.

The source code can be obtained via the Downloads page and as described below under Getting the source. The primary dependency is numpy.

Please read through this whole document. Installing MDAnalysis is unfortunately not always absolutely straightforward because of the various dependencies on other packages. InstallRecipes collects a number of examples of how MDAnalysis has been successfully installed on various systems; possibly one of the recipes applies to your situation, too, and you can simply copy and paste.

Getting the source

You can either get the source tar files or check out the source code from the git repository.

Source tar files

In order to download the source packages, you need to go to the PyPI repositories:

• https://pypi.python.org/pypi/MDAnalysis (main package)
• https://pypi.python.org/pypi/MDAnalysisTests (for the tests) and download the tar files from there.

Git repository

Alternatively, you can check out the MDAnalysis directory from the git repository at https://github.com/MDAnalysis/mdanalysis. In most cases simply do

git clone https://github.com/MDAnalysis/mdanalysis
cd mdanalysis

If you have cloned the repository before, all you need to do is

git pull

to update your files.

Standard installation from source

If you want to install MDAnalysis from source you will need a C compiler.

We recommend (for python >= 2.7) the following way of installing in your home directory (a so called "user" installation) ::

python setup.py build
python setup.py install --user

If you want to install in the system wide python directory you will probably require administrative privileges, and so do

sudo python setup.py install

It is also possible to use --prefix, --home, or --user options for setup.py to install in a different (probably your private) python directory hierarchy.

If you have problem at this stage then have a look at the operating system specific notes at the end of this file or look in the issue tracker --- maybe the problem is recognized and a workaround can be found in the comments

If you have problems ask on the mailing list.

pip

One can also use pip. For all releases, you should be able to just do

pip --upgrade MDAnalysis 
pip --upgrade MDAnalysisTests

and pip will download the source distribution from the Python package index and install them, together with any required dependencies.

If you want to install from the checked out source, you can also use pip:

pip [options] ./mdanalysis

for a standard installation.

Developer installation

A developer installation (that immediately reflects changes to the sources) can be done with

cd ./mdanalysis/package
python setup develop [options]

For testing one can simply use

python setup.py develop --install-dir=$HOME/python-lib/ --script-dir=$HOME/bin

This builds and installs a working version in ~/python-lib/MDAnalysis which is linked to the unpacked source. Then add $HOME/python-lib to the PYTHONPATH

export PYTHONPATH=${PYTHONPATH}:$HOME/python-lib

However, the developer installation above is probably cleaner.