https://github.com/becksteinlab/parallel-analysis-in-the-mdanalysis-library
Benchmarking MDAnalysis with Dask (and MPI). Supplementary Information for SciPy 2017 paper.
https://github.com/becksteinlab/parallel-analysis-in-the-mdanalysis-library
benchmark dask mdanalysis mpi trajectory
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Benchmarking MDAnalysis with Dask (and MPI). Supplementary Information for SciPy 2017 paper.
- Host: GitHub
- URL: https://github.com/becksteinlab/parallel-analysis-in-the-mdanalysis-library
- Owner: Becksteinlab
- License: mit
- Created: 2017-02-27T20:18:31.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2017-10-12T00:56:08.000Z (over 7 years ago)
- Last Synced: 2025-04-02T06:43:11.836Z (about 2 months ago)
- Topics: benchmark, dask, mdanalysis, mpi, trajectory
- Language: Python
- Homepage: http://conference.scipy.org/proceedings/scipy2017/mahzad_khoslessan.html
- Size: 78.1 KB
- Stars: 3
- Watchers: 3
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Parallel analysis in the MDAnalysis Library
We present a benchmark suite that can be used to evaluate performance for
parallel map-reduce type analysis and use it to investigate the performance of
[MDAnalysis][] with the [Dask][] library for task-graph based computing
[(Khoslessan et al, 2017)][KhoshlessanScipy2017].
A range of commonly used MD file formats (CHARMM/NAMD DCD, Gromacs XTC, Amber NetCDF) and different
trajectory sizes are tested on different high-performance computing (HPC)
resources. Benchmarks are performed both on a single node and across multiple
nodes.
For space reasons, not all data could be shown in the SciPy 2017 conference proceedings
paper. For a full analysis see the Technical Report [(Khoshlessan and Beckstein, 2017)][Khoshlessan2017].
The report is available on figshare at DOI [10.6084/m9.figshare.4695742][].
## Supplementary information for SciPy 2017 paper
This repository should be considered part of the Supplementary information to the SciPy 2017 Proceedings
paper [(Khoslessan et al, 2017)][KhoshlessanScipy2017].
### Benchmarking code
The repository contain the code to benchmark parallelization of [MDAnalysis][]:
* RMSD calculation with MDAnalysis with Dask for XTC, DCD, NCDF
* RMSD calculation with MDAnalysis with MPI
### Data files
The data files consist of a topology file `adk4AKE.psf` (in CHARMM PSF format; N = 3341 atoms)
and a trajectory `1ake_007-nowater-core-dt240ps.dcd` (DCD format) of length 1.004 μs with
4187 frames; both are freely available under the CC-BY license from figshare at DOI [10.6084/m9.figshare.5108170][]
Files in XTC and NetCDF formats are generated from the DCD.
## Tested libraries
* [MDAnalysis][] 0.15.0
* [Dask][] 0.12.0 (also 0.13.0)
* [Distributed][] 1.14.3 (also 1.15.1)
* [NumPy][] 1.11.2 (also 1.12.0)
## Comments and Questions
Please raise issues in the [issue tracker][] or ask on the
[MDAnalysis developer mailing list][].
## References
[KhoshlessanScipy2017]: #KhoshlessanScipy2017
M. Khoshlessan, I. Paraskevakos, S. Jha, and O. Beckstein (2017).
[_Parallel analysis in MDAnalysis using the Dask parallel computing library_](http://conference.scipy.org/proceedings/scipy2017/mahzad_khoslessan.html).
In S. Benthall and S. Rostrup, editors, Proceedings of the 16th Python in Science Conference, Austin, TX, 2017. SciPy.
[Khoshlessan2017]: #Khoshlessan2017
Khoshlessan, Mahzad; Beckstein, Oliver (2017): _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][]
[MDAnalysis]: http://mdanalysis.org
[Dask]: http://dask.pydata.org
[Distributed]: https://distributed.readthedocs.io/
[NumPy]: http://numpy.scipy.org/
[issue tracker]: https://github.com/Becksteinlab/Parallel-analysis-in-the-MDAnalysis-Library/issues
[MDAnalysis developer mailing list]: http://developers.mdanalysis.org/
[10.6084/m9.figshare.4695742]: https://doi.org/10.6084/m9.figshare.4695742
[10.6084/m9.figshare.5108170]: https://doi.org/10.6084/m9.figshare.5108170
[adk4AKE.psf]: https://www.dropbox.com/sh/ln0klc9j7mhvxkg/AAAL5eP1vrn0tK-67qVDnKeua/Trajectories/equilibrium/adk4AKE.psf
[1ake_007-nowater-core-dt240ps.dcd]: https://www.dropbox.com/sh/ln0klc9j7mhvxkg/AABSaNJ0fRFgY1UfxIH_jWtka/Trajectories/equilibrium/1ake_007-nowater-core-dt240ps.dcd