[PRE REVIEW]: MPI-Rockstar: a Hybrid MPI and OpenMP Parallel Implementation of the Rockstar Halo finder

[editorialbot]

Submitting author: @Tomoaki-Ishiyama (Tomoaki Ishiyama)
Repository: https://github.com/Tomoaki-Ishiyama/mpi-rockstar
Branch with paper.md (empty if default branch): joss
Version: v1.0.0
Editor: @junghans
Reviewers: Pending
Managing EiC: Warrick Ball

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[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1093/pasj/61.6.1319 is OK
- 10.1093/mnras/stab1755 is OK
- 10.1186/s40668-017-0021-1 is OK
- 10.1093/mnras/stac3072 is OK
- 10.1088/0004-637X/762/2/109 is OK
- 10.1088/1674-4527/18/6/62 is OK
- 10.1093/mnras/stt1403 is OK
- 10.1017/pasa.2019.12 is OK
- 10.1093/mnras/stab2482 is OK
- 10.1093/mnras/stab1855 is OK
- 10.1088/0067-0049/182/2/608 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: 4.45 Pflops astrophysical N-body simulation on K c...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.05 s (1830.8 files/s, 318894.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C                               42           1253            377          10168
C++                              1            321             76           1633
C/C++ Header                    44            286             68           1357
TeX                              1             32              0            225
Markdown                         2             47              0            197
Perl                             1             27              5            178
YAML                             2              4              8             46
make                             1             16              3             46
-------------------------------------------------------------------------------
SUM:                            94           1986            537          13850
-------------------------------------------------------------------------------

Commit count by author:

    58	Tomoaki-Ishiyama
    24	Ken Osato
     2	stanaka

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 584

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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[warrickball]

Hi @Tomoaki-Ishiyama, and thanks for your submission to JOSS. The nature of this submission looks a bit unusual so I'd like to clear up a few things before we consider continuing to review. Specifically, is the idea that JOSS reviews the submitted repo and the original Rockstar code? Or is this submission in effect a standalone fork that extends the previous code?

The latter is in principle in scope for JOSS (see Should I write my own software or contribute to an existing package?) but I notice that the new documentation is just the top-level README, which has some technical details but little context, and there don't appear to be any examples ready to run out-of-the-box. You might find inspiration for the kind of documentation and examples we strive for by glancing at some of the similar articles listed in the comment above.

[Tomoaki-Ishiyama]

Hi @warrickball and thank you so much for your comments. This submission is in effect a standalone fork that extends the original Rockstar code.

Indeed, the current README contains little context. We will attempt to fix it as soon as possible.

[warrickball]

Thanks. In that case, I'm going to flag this article for an editorial review of whether the extension to MPI meets JOSS requirements for substantial scholarly effort. This should take about two weeks. Sorry for the extra wait!

[warrickball]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Tomoaki-Ishiyama]

We believe that this code meets JOSS requirements because the extension to MPI and massively parallel environment took nearly a year and our community was eager for this extension. Thank you for your consideration.

[warrickball]

Hi again @Tomoaki-Ishiyama, I'm pleased to say that the editorial board has agreed that the MPI parallelisation alone is a substantial contribution, so we'll continue our process. All the suitable JOSS editors are currently working at capacity so I'm going to "waitlist" this review until an editor with the relevant expertise is available to take it on. Thanks for your patience!

[Tomoaki-Ishiyama]

@warrickball That's great! Thank you so much. Then, we will wait the editor assignment.

[Tomoaki-Ishiyama]

@warrickball We have been waiting the editor assignment for more than 3 months. How much longer do we have to wait? Editors seem to be assigned for the most of papers submitted after us. Thank you for your assistance.

[warrickball]

Hi @Tomoaki-Ishiyama, I do apologise for the very long wait. The Astronomy, Astrophysics & Space Science (AASS) track of JOSS has a substantial backlog, which is typically leading to a ~3 month wait from submission to an editor becoming available. MPI-Rockstar is now in effect at the front of the queue but we still need an editor with appropriate expertise to become available, which is why some more recent submissions (though many also >2 months old) have been picked up first.

[junghans]

@warrickball I can help to edit this.

[warrickball]

@junghans, that'd be great! You're more than welcome to self-assign yourself as editor. Feel free to ask me anything (here or privately) before you self-assign.

[junghans]

@editorialbot assign me as editor

[editorialbot]

Assigned! @junghans is now the editor

[junghans]

@Tomoaki-Ishiyama at a first glance the paper rather short, could you add a section with details on how the parallelization was done? And maybe some scaling results?

See https://doi.org/[10.21105/joss.03296](https://doi.org/10.21105/joss.03296) and https://doi.org/[10.21105/joss.06714](https://doi.org/10.21105/joss.06714)

[Tomoaki-Ishiyama]

@junghans Thank you for your assistance! I see. I will add a section for the parallelization and scalability as soon as possible.

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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[Tomoaki-Ishiyama]

@junghans I have just updated the draft following your comments. Please review it again.

[junghans]

@junghans I have just updated the draft following your comments. Please review it again.

Thanks for adding that section, could you please also add a figure showing the hybrid parallelization scheme?