Parallel Molecular Dynamics Analysis tools
Project description
Ready to use analysis and buildings blocks to write parallel analysis algorithms using MDAnalysis with dask.
For example, run a rmsd analysis on all available cores:
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
pip install --upgrade pmdaDevelopment version from source
To install the latest development version from source, run
git clone git@github.com:MDAnalysis/pmda.git
cd pmda
python setup.py installGetting help
Help is also available through the MDAnalysis mailing list
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].
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
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