{"id":19339538,"url":"https://github.com/becksteinlab/parallel-analysis-in-the-mdanalysis-library","last_synced_at":"2025-04-23T02:30:48.681Z","repository":{"id":112683652,"uuid":"83352631","full_name":"Becksteinlab/Parallel-analysis-in-the-MDAnalysis-Library","owner":"Becksteinlab","description":"Benchmarking MDAnalysis with Dask (and MPI). 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Benchmarks are performed both on a single node and across multiple\nnodes.\n\nFor space reasons, not all data could be shown in the SciPy 2017 conference proceedings\npaper. For a full analysis see the Technical Report [(Khoshlessan and Beckstein, 2017)][Khoshlessan2017].\nThe report is available on figshare at DOI [10.6084/m9.figshare.4695742][].\n\n\n## Supplementary information for SciPy 2017 paper\nThis repository should be considered part of the Supplementary information to the SciPy 2017 Proceedings\npaper [(Khoslessan et al, 2017)][KhoshlessanScipy2017].\n\n### Benchmarking code\n\nThe repository contain the code to benchmark parallelization of [MDAnalysis][]:\n* RMSD calculation with MDAnalysis with Dask for XTC, DCD, NCDF\n* RMSD calculation with MDAnalysis with MPI\n\n### Data files\n\nThe data files consist of a topology file `adk4AKE.psf` (in CHARMM PSF format; N = 3341 atoms) \nand a trajectory `1ake_007-nowater-core-dt240ps.dcd` (DCD format) of length 1.004 μs with \n4187 frames; both are freely available under the CC-BY license from figshare at DOI [10.6084/m9.figshare.5108170][] \n\nFiles in XTC and NetCDF formats are generated from the DCD.\n\n## Tested libraries\n\n* [MDAnalysis][] 0.15.0\n* [Dask][] 0.12.0 (also 0.13.0)\n* [Distributed][] 1.14.3 (also 1.15.1)\n* [NumPy][] 1.11.2 (also 1.12.0)\n\n## Comments and Questions\n\nPlease raise issues in the [issue tracker][] or ask on the\n[MDAnalysis developer mailing list][].\n\n\n## References\n\n[KhoshlessanScipy2017]: #KhoshlessanScipy2017\n\u003ca name=\"KhoshlessanScipy2017\"\u003eM. Khoshlessan, I. Paraskevakos, S. Jha, and O. Beckstein (2017)\u003c/a\u003e. \n[_Parallel analysis in MDAnalysis using the Dask parallel computing library_](http://conference.scipy.org/proceedings/scipy2017/mahzad_khoslessan.html).\nIn S. Benthall and S. Rostrup, editors, Proceedings of the 16th Python in Science Conference, Austin, TX, 2017. SciPy. \n   \n[Khoshlessan2017]: #Khoshlessan2017\n\u003ca name=\"Khoshlessan2017\"\u003eKhoshlessan, Mahzad; Beckstein, Oliver (2017)\u003c/a\u003e: _Parallel analysis in the MDAnalysis Library: Benchmark of\nTrajectory File Formats._ Technical report, Arizona State University, Tempe, AZ, 2017. figshare. doi:[10.6084/m9.figshare.4695742][]\n\n\n[MDAnalysis]: http://mdanalysis.org\n[Dask]: http://dask.pydata.org\n[Distributed]: https://distributed.readthedocs.io/\n[NumPy]: http://numpy.scipy.org/\n[issue tracker]: https://github.com/Becksteinlab/Parallel-analysis-in-the-MDAnalysis-Library/issues\n[MDAnalysis developer mailing list]: http://developers.mdanalysis.org/\n[10.6084/m9.figshare.4695742]: https://doi.org/10.6084/m9.figshare.4695742\n[10.6084/m9.figshare.5108170]: https://doi.org/10.6084/m9.figshare.5108170\n\n\n[adk4AKE.psf]:    https://www.dropbox.com/sh/ln0klc9j7mhvxkg/AAAL5eP1vrn0tK-67qVDnKeua/Trajectories/equilibrium/adk4AKE.psf\n[1ake_007-nowater-core-dt240ps.dcd]: https://www.dropbox.com/sh/ln0klc9j7mhvxkg/AABSaNJ0fRFgY1UfxIH_jWtka/Trajectories/equilibrium/1ake_007-nowater-core-dt240ps.dcd\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fparallel-analysis-in-the-mdanalysis-library","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbecksteinlab%2Fparallel-analysis-in-the-mdanalysis-library","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fparallel-analysis-in-the-mdanalysis-library/lists"}