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https://github.com/mdanalysis/pmda

Parallel algorithms for MDAnalysis
https://github.com/mdanalysis/pmda

analysis dask mdanalysis molecular-dynamics parallel

Last synced: 6 days ago
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Parallel algorithms for MDAnalysis

Host: GitHub
URL: https://github.com/mdanalysis/pmda
Owner: MDAnalysis
License: other
Created: 2017-10-09T23:46:26.000Z (over 7 years ago)
Default Branch: master
Last Pushed: 2024-08-02T17:48:40.000Z (6 months ago)
Last Synced: 2025-01-21T00:12:31.758Z (14 days ago)
Topics: analysis, dask, mdanalysis, molecular-dynamics, parallel
Language: Python
Homepage: https://www.mdanalysis.org/pmda/
Size: 6.71 MB
Stars: 31
Watchers: 14
Forks: 23
Open Issues: 37
Metadata Files:
- Readme: README.rst
- Changelog: CHANGELOG
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Authors: AUTHORS

Awesome Lists containing this project

README

        ==============================================

  PMDA - Parallel Molecular Dynamics Analysis

==============================================

|build| |cov| |PRwelcome| |zenodo| |conda|

Ready to use analysis and buildings blocks to write parallel analysis algorithms

using MDAnalysis_ with dask_.

.. warning::

   This project is **alpha software** and not API stable. It will and

   should rapidly evolve to test different approaches to implementing

   parallel analysis in a seamless and intuitive fashion.

For example, run a rmsd analysis on all available cores:

.. code:: python

   import MDAnalysis as mda

   from pmda import rms

   u = mda.Universe(top, traj)

   ref = mda.Universe(top, traj)

   rmsd_ana = rms.RMSD(u.atoms, ref.atoms).run(n_jobs=-1)

   print(rmsd_ana.rmsd)

By default PMDA use the multiprocessing scheduler of dask_. This is sufficient

if you want to run your simulation on a single machine. If your analysis takes

a very long time (>30 min) you can also spread it to several nodes using the

distributed_ scheduler. To do this you can pass a ``scheduler`` keyword

argument to the ``run`` method.

To write your own parallel algorithms you can subclass the

``pmda.parallel.ParallelAnalysisBase`` class.

License and source code

=======================

PMDA is released under the `GNU General Public License, version 2`_ (see the

files AUTHORS and LICENSE for details).

Source code is available in the public GitHub repository

https://github.com/MDAnalysis/pmda/.

       

Installation

============

Install a release with ``pip``

------------------------------

The latest release is available from https://pypi.org/project/pmda/

and can be installed with pip_

.. code-block:: sh

   pip install --upgrade pmda

		

   

Development version from source

-------------------------------

To install the latest development version from source, run

.. code-block:: sh

  git clone [email protected]:MDAnalysis/pmda.git

  cd pmda

  python setup.py install

 

Getting help

============

*Help* is also available through the *MDAnalysis mailing list*

     https://groups.google.com/group/mdnalysis-discussion

Please report *bugs and feature requests* for PMDA through the `Issue

Tracker`_.

Contributing

============

PMDA welcomes new contributions. Please drop by the `MDAnalysis developer

mailing list`_ to discuss and ask questions.

To contribute code, submit a *pull request* against the master branch in the

`PMDA repository`_.

Citation

========

If you use PMDA in published work please cite [Fan2019]_.

.. [Fan2019] Shujie Fan, Max Linke, Ioannis Paraskevakos, Richard J. Gowers,

	     Michael Gecht, and Oliver Beckstein. PMDA --- Parallel Molecular Dynamics

	     Analysis. In Chris Calloway, David Lippa, Dillon Niederhut, and David Shupe,

	     editors, Proceedings of the 18th Python in Science Conference,

	     pages 134-142, Austin, TX, 2019.

	     doi: `10.25080/Majora-7ddc1dd1-013`_	     

.. _MDAnalysis: https://www.mdanalysis.org

.. _dask: https://dask.pydata.org/en/latest/

.. _distributed: https://distributed.readthedocs.io/

.. _`Issue tracker`: https://github.com/MDAnalysis/pmda/issues

.. _`PMDA repository`: https://github.com/MDAnalysis/pmda/

.. _pip: https://pip.pypa.io/en/stable/

.. _`GNU General Public License, version 2`:

   https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html

.. _`MDAnalysis developer mailing list`:

   https://groups.google.com/group/mdnalysis-devel

.. _`10.25080/Majora-7ddc1dd1-013`:

   https://doi.org/10.25080/Majora-7ddc1dd1-013

   

.. |build| image:: https://travis-ci.org/MDAnalysis/pmda.svg?branch=master

    :alt: Build Status

    :target: https://travis-ci.org/MDAnalysis/pmda

.. |cov| image:: https://codecov.io/gh/MDAnalysis/pmda/branch/master/graph/badge.svg

   :alt: Coverage

   :target: https://codecov.io/gh/MDAnalysis/pmda

.. |zenodo| image:: https://zenodo.org/badge/106346721.svg

   :alt: DOI

   :target: https://zenodo.org/badge/latestdoi/106346721

.. |conda| image:: https://anaconda.org/conda-forge/pmda/badges/version.svg

   :alt: conda release

   :target: https://anaconda.org/conda-forge/pmda

.. |PRwelcome| image:: https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square

   :alt: PRs welcome

   :target: http://makeapullrequest.com