Installing MDSynthesis

Since MDSynthesis requires datreant.data, which uses HDF5 as the file format of choice for persistence, you will first need to install the HDF5 libraries either using your package manager or manually.

On Ubuntu 14.04 this will be

apt-get install libhdf5-serial-1.8.4 libhdf5-serial-dev

and on Arch Linux

pacman -S hdf5

You can then install MDSynthesis from PyPI using pip:

pip install mdsynthesis

It is also possible to use --user to install into your user’s site-packages directory:

pip install --user mdsynthesis

Be aware that some dependencies may require numpy and/or Cython to be installed beforehand!

Installing using Conda

We also provide conda packages. Using the conda packages has the advantage that they contain the hdf5 library, so you can install MDSynthesis easily on all unix systems including macOS. To install MDSynthesis with conda type:

conda install -c datreant mdsynthesis

Dependencies

The dependencies of MDSynthesis are:

Installing from source

To install from source, clone the repository and switch to the master branch

git clone git@github.com:datreant/MDSynthesis.git
cd MDSynthesis
git checkout master

Installation of the packages is as simple as

pip install .

which installs mdsynthesis in the system wide python directory (this may require administrative privileges).

It is also possible to use --user to install into your user’s site-packages directory:

pip install --user .