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Paper: PMDA – Parallel Molecular Dynamics Analysis #476

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commented May 23, 2019

Dear Editors,

Please consider our contribution to SciPy 2019, PMDA – Parallel Molecular Dynamics Analysis by Shujie Fan @VOD555 , Max Linke @kain88-de , Ioannis Paraskevakos @iparask , Richard J. Gowers @richardjgowers, Michael Gecht @mimischi, Oliver Beckstein @orbeckst

Thank you,
Oliver Beckstein


If you are creating this PR in order to submit a draft of your paper,
see http://procbuild.scipy.org/ for logs generated by the build
process.

See the project readme
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VOD555 and others added some commits May 17, 2019

Rearrange With pmda.parallel.ParallelAnalysisBase
 - Rearrange the processes to build the user-defined analysis tasks.
first two introductory paragraphs + XSEDE ack
- MD
- analysis, becoming bottleneck
- basic idea of PMDA
- added XSEDE to acknowledgements
introduction v1
- code availability and development process (can be moved elsewhere)
- key idea of PMDA

orbeckst and others added some commits Jun 13, 2019

methods updates
- moved software version to Benchmark Environment (to improve logic and flow)
- more precise desrciption of SDSC Comet
installation details
see #36 --- depending on @VOD555 's comments this commit needs to be changed
re-arranged performance evaluation section
- followed reviewer @cyrush 's recommendation #476 (comment)
  to change the order so that benchmarking method directly follows benchmarking results (thank you!)
- close #32
- replaced 'Results & Discussion' with 'Performance Evaluation' and integrated the "methods" part;
  this had the advantage that the sectioning became clearer, some duplicated text could be removed,
  and that the logical flow is much better
- various smaller text fixes/improvements
cleaned up bib file
- manually removed URL fields when it replicated DOI
- fixed DOIs
- removed bibdesk (url/file) fields

All done manually with Emacs regex search and replace...
updated text for plots with error bars
- updated Methods (everything 5 repeats, plot means and stdev)
- updated Results: refer to the new figures
- updated captions to explain mean + stdev error bars
- include reference to Gustafson-Baris (could do more, see #28, but no time and space)
- minor readability fixes
- close #27
@deniederhut

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commented Jun 20, 2019

@orbeckst feel free to @ your reviewers when you feel this is ready for a second look 😄

integrate stacked fraction of time plots
- add fraction of time plots for Lustre-distributed-3node
  - RMSD
  - RDF
  as suggested by reviewer @cyrush  in #476 (comment)
- add text for the plots, comment on parallelizable fraction
- include reference to Amdahl's law (could do more, see #28, but no time and space)
- close #33
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commented Jun 20, 2019

@cyrush we addressed your comments, including the stacked plots (Becksteinlab#33). They are a really good addition to the paper. Thank you for the suggestion. Can we acknowledge you in the paper for the idea? (I will add a commit so that you can see what we would want to add.) Thanks again.

orbeckst and others added some commits Jun 20, 2019

updated computational details for RDF calculation
- close #30
- add details for cut-off and bins
- fixed: number of distance calculations is O(N) and not O(N^2) because we use a cut-off
  (capped_distances() in the RDF calculation)
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commented Jun 21, 2019

All last-minute edits done.

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commented Jun 24, 2019

@orbeckst @VOD555 thank you for the updates and for taking the time to create the extra plots.
The stack % plots really help present the scalability of your test cases. Thanks for the acknowledgment as well!

@deniederhut I strongly support including this paper the proceedings. In my view, authors went above and beyond our suggestions to strengthen an already well written paper.

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commented Jun 25, 2019

Awesome. Thanks everyone!

@deniederhut deniederhut added ready and removed pending-comment labels Jun 25, 2019

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