PMDA - Parallel Molecular Dynamics Analysis¶
- Release
0.3.0+21.g6c037c8
- Date
Oct 18, 2020
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:
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 uses the multiprocessing scheduler of Dask. This is sufficient if you want to run your simulation on a single machine although you may use any of the single-machine schedulers that Dask supports. If your analysis takes a long time you can also spread it to several nodes using the distributed scheduler (see Parallelization for more details).
To write your own parallel algorithms you can subclass the
ParallelAnalysisBase class (see
Writing new parallel analysis for more details).
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¶
The easiest way to install PMDA is as a conda package and will result in a complete installation on Linux, macOS, and Windows 1. If you have not installed Python packages before, we recommend that you perform the conda installation.
PMDA runs under Python 3.4 or higher or Python 2.7 on Linux, macOS, and Windows 1.
Install a release with conda¶
First installation with conda:
conda config --add channels conda-forge
conda install pmda
which will automatically install a full set of dependencies (including MDAnalysis, Dask, and distributed).
To upgrade later:
conda update pmda
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 pmda
Development version from source¶
To install the latest development version from source, run
git clone [email protected]:MDAnalysis/pmda.git
cd pmda
python setup.py install
Getting 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.