https://github.com/becksteinlab/mdanalysis-with-dask

Benchmarking MDAnalysis with dask.
https://github.com/becksteinlab/mdanalysis-with-dask

dask hpc mdanalysis molecular-dynamics-simulation mpi python spidal

Last synced: about 1 month ago
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Benchmarking MDAnalysis with dask.

• Host: GitHub
• URL: https://github.com/becksteinlab/mdanalysis-with-dask
• Owner: Becksteinlab
• License: gpl-3.0
• Created: 2017-05-26T15:07:57.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2017-09-01T01:20:00.000Z (over 7 years ago)
• Last Synced: 2025-04-02T06:43:07.922Z (about 2 months ago)
• Topics: dask, hpc, mdanalysis, molecular-dynamics-simulation, mpi, python, spidal
• Language: Python
• Homepage:
• Size: 1.15 MB
• Stars: 5
• Watchers: 5
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# MDAnalysis with Dask #

Code to benchmark parallelization of

[MDAnalysis](http://mdanalysis.org) with

[Dask](http://dask.pydata.org/) [1, 2, 3] 

## References ##

1. M. Khoshlessan and O. Beckstein. Parallel analysis in the

   MDAnalysis library: Benchmark of trajectory file formats. Technical

   report, Arizona State University, Tempe, AZ, 2017. figshare. doi:

   [10.6084/m9.figshare.4695742](https://doi.org/10.6084/m9.figshare.4695742)

2. M. Khoshlessan, I. Paraskevakos, S. Jha, and

   O. Beckstein. Parallel analysis in MDAnalysis using the Dask

   parallel computing library. In S. Benthall and S. Rostrup, editors,

   Proceedings of the 16th Python in Science Conference, Austin,

   TX, 2017. SciPy. 

   [PR scipy-conference/scipy_proceedings#290](https://github.com/scipy-conference/scipy_proceedings/pull/290)

3. I. Paraskevakos et al, [Parallel Analysis of Molecular Dynamics Trajectory](https://github.com/radical-papers/midas-paper/tree/master/2016-eScience). In preparation.