Sire

About

Sire is a free, open source, multiscale molecular simulation framework, written to allow computational modellers to quickly prototype and develop new algorithms for molecular simulation and molecular design. Sire is written as a collection of libraries, each of which contains self-contained and robust C++/Python building blocks. These building blocks are vectorised and thread-aware and can be streamed (saved/loaded) to and from a version-controlled and tagged binary format, thereby allowing them to be combined together easily to build custom multi-processor molecular simulation applications.

For more information about how to use Sire, and about application built with Sire, please visit the Sire website.

Installation

The easiest way to install Sire is using our conda channel. Sire is built using dependencies from conda-forge, so please ensure that the channel takes strict priority. We recommend using Miniforge.

To create a new environment:

conda create -n sire -c conda-forge -c michellab sire
conda activate sire

To install the latest development version you can use:

conda create -n sire-dev -c conda-forge -c michellab/label/dev sire
conda activate sire-dev

If you find that Conda is particularly slow to install or upgrade, then we advise using mamba:

conda install -c conda-forge mamba

You can then replace all conda commands with mamba, e.g.:

mamba create -n sire -c conda-forge -c michellab sire

However, as you are here, it is likely you want to download the latest, greatest version of the code, which you will need to compile. To compile Sire, you need a Git client to download the source, and a working internet connection (needed by the Sire compilation scripts to download additional dependencies).

First, you need to create and activate a conda environment, e.g.

conda create -n sire-dev
conda activate sire-dev

We find that Conda is particularly slow to install or upgrade, so we advise installing mamba:

conda install -c conda-forge mamba

Next, you need to install the Sire build dependencies.

mamba install cmake pip-requirements-parser

You will also need to install compilers, e.g. on Linux use

mamba install gcc gxx

on MacOS use

mamba install clang clangxx

and on Windows use

mamba install conda-build

Next, you can clone the Sire source code and compile and install Sire:

git clone git@github.com:michellab/Sire.git
cd Sire
python setup.py install

A small word of warning, the compilation can easily take over an hour!

The above will compile Sire in your existing conda environment.

If you plan to build BioSimSpace on top of Sire, then you will need to resolve BioSimSpace's dependencies at the time Sire is installed to ensure that it is built in a self-consistent way. This can be achieved as follows:

python setup.py --install-bss-deps install

Support and Development

Bugs, Comments, Questions

For bug reports/sugguestions/complains please file an issue on GitHub. or contact the developers via the google user group: https://groups.google.com/forum/#!forum/sire-users

Developers guide

Please visit the website for information on how to develop applications using Sire.

GitHub actions

Since Sire is quite large, a build can take quite long and might not be neccessary if a commit is only fixing a couple of typos. Simply add ci skip to your commit message and GitHub actions will not invoke an autobuild.

Note that every time you commit to devel, it will trigger a build of Sire, full testing, construction of a Conda package and upload to our Anaconda channel. Please think twice before committing directly to devel. You should ideally be working in a _feature_ branch, and only commit to devel once you are happy the code works on your branch. Use ci skip until you are happy that you want to trigger a full build, test and deployment. This full pipeline will take several hours to complete.

Have fun :-)