[PRE REVIEW]: PyLops-MPI - MPI Powered PyLops with mpi4py

[editorialbot]

Submitting author: @rohanbabbar04 (Rohan Babbar)
Repository: https://github.com/PyLops/pylops-mpi
Branch with paper.md (empty if default branch): joss
Version: v0.1.0
Editor: @gkthiruvathukal
Reviewers: @gonsie, @mikaem
Managing EiC: Daniel S. Katz

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/be7da46cc87d0c182b26862b77a6e608/status.svg)](https://joss.theoj.org/papers/be7da46cc87d0c182b26862b77a6e608)

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[editorialbot]

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

✅ OK DOIs

- 10.1016/j.softx.2019.100361 is OK
- 10.1109/MCSE.2021.3083216 is OK
- 10.21105/joss.01340 is OK
- 10.21105/joss.06415 is OK
- 10.21105/joss.03419 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1093/gji/ggab388 is OK
- 10.1109/tgrs.2022.3179626 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

❌ MISSING DOIs

- 10.1190/1.1444517 may be a valid DOI for title: Least-squares migration of incomplete reflection d...

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1162.5 files/s, 152316.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          40           1140           2091           4702
reStructuredText                17            300            279            394
Markdown                         3             58              0            229
YAML                             7             13             12            182
TeX                              1              9              0            121
CSS                              2             24              7             91
make                             2             18              9             49
TOML                             1              3              0             41
HTML                             1              6              0             32
Bourne Shell                     1              3              2             12
-------------------------------------------------------------------------------
SUM:                            75           1574           2400           5853
-------------------------------------------------------------------------------

Commit count by author:

   183	rohanbabbar04
    44	mrava87
    23	Rohan Babbar
     4	Matteo Ravasi

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1822

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU Lesser General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

mpi4jax: Zero-copy MPI communication of JAX arrays
Submitting author: @dionhaefner
Handling editor: @kellyrowland (Active)
Reviewers: @1313e, @Himscipy
Similarity score: 0.6752

GridapDistributed: a massively parallel finite element toolbox in Julia
Submitting author: @amartinhuertas
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @PetrKryslUCSD, @Leticia-maria, @jedbrown
Similarity score: 0.6702

mpi4py-fft: Parallel Fast Fourier Transforms with MPI for Python
Submitting author: @mikaem
Handling editor: @VivianePons (Retired)
Reviewers: @iljah, @rainwoodman
Similarity score: 0.6702

pyOptSparse: A Python framework for large-scale constrained nonlinear optimization of sparse systems
Submitting author: @nwu63
Handling editor: @poulson (Retired)
Reviewers: @jgoldfar, @vissarion, @matbesancon
Similarity score: 0.6689

shmem4py: OpenSHMEM for Python
Submitting author: @mrogowski
Handling editor: @danielskatz (Active)
Reviewers: @greghbauer, @gonsie
Similarity score: 0.6682

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[rohanbabbar04]

@editorialbot commands

[editorialbot]

Hello @rohanbabbar04, here are the things you can ask me to do:

# List all available commands
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# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
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@editorialbot generate pdf

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@editorialbot generate preprint

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@editorialbot list reviewers

[rohanbabbar04]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1016/j.softx.2019.100361 is OK
- 10.1109/MCSE.2021.3083216 is OK
- 10.21105/joss.01340 is OK
- 10.21105/joss.06415 is OK
- 10.21105/joss.03419 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1093/gji/ggab388 is OK
- 10.1190/1.1444517 is OK
- 10.1109/tgrs.2022.3179626 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[rohanbabbar04]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

mpi4jax: Zero-copy MPI communication of JAX arrays
Submitting author: @dionhaefner
Handling editor: @kellyrowland (Active)
Reviewers: @1313e, @Himscipy
Similarity score: 0.6755

mpi4py-fft: Parallel Fast Fourier Transforms with MPI for Python
Submitting author: @mikaem
Handling editor: @VivianePons (Retired)
Reviewers: @iljah, @rainwoodman
Similarity score: 0.6702

GridapDistributed: a massively parallel finite element toolbox in Julia
Submitting author: @amartinhuertas
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @PetrKryslUCSD, @Leticia-maria, @jedbrown
Similarity score: 0.6701

pyOptSparse: A Python framework for large-scale constrained nonlinear optimization of sparse systems
Submitting author: @nwu63
Handling editor: @poulson (Retired)
Reviewers: @jgoldfar, @vissarion, @matbesancon
Similarity score: 0.6689

shmem4py: OpenSHMEM for Python
Submitting author: @mrogowski
Handling editor: @danielskatz (Active)
Reviewers: @greghbauer, @gonsie
Similarity score: 0.6685

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danielskatz]

@rohanbabbar04 - thanks for your submission. I'll be the track editor, working on it until it gets assigned to an editor, and then coming back at the end to handle final processing.

At this point, can you

1. ensure that references have spaces before them in the .md file, so that we don't have things like where the space is missing in the PDF
2. Consider removing some of your paper in favor of pointing to documentation in the repo. Your paper is about 1800 words, and JOSS papers are recommended to be 250-1000 words.
3. Consider if you need an Acknowledgments section, to acknowledge any funding or other support or help

I'll mark this as paused - please ping me when you are ready to proceed or have questions.

[rohanbabbar04]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1195.3 files/s, 155625.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          40           1140           2091           4702
reStructuredText                17            300            279            394
YAML                             7             13             12            182
Markdown                         3             50              0            171
TeX                              1              9              0            125
CSS                              2             24              7             91
make                             2             18              9             49
TOML                             1              3              0             41
HTML                             1              6              0             32
Bourne Shell                     1              3              2             12
-------------------------------------------------------------------------------
SUM:                            75           1566           2400           5799
-------------------------------------------------------------------------------

Commit count by author:

   185	rohanbabbar04
    44	mrava87
    24	Rohan Babbar
     4	Matteo Ravasi

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1009

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU Lesser General Public License v3.0 (Check here for OSI approval)

[rohanbabbar04]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

shmem4py: OpenSHMEM for Python
Submitting author: @mrogowski
Handling editor: @danielskatz (Active)
Reviewers: @greghbauer, @gonsie
Similarity score: 0.7771

X-PSI: A Python package for neutron star X-ray pulse simulation and inference
Submitting author: @drannawatts
Handling editor: @adonath (Active)
Reviewers: @JohannesBuchner, @matteobachetti
Similarity score: 0.7575

mpi4jax: Zero-copy MPI communication of JAX arrays
Submitting author: @dionhaefner
Handling editor: @kellyrowland (Active)
Reviewers: @1313e, @Himscipy
Similarity score: 0.7410

parafields: A generator for distributed, stationary Gaussian processes
Submitting author: @dokempf
Handling editor: @diehlpk (Active)
Reviewers: @shahmoradi, @gchure
Similarity score: 0.7354

Micro Manager: a Python package for adaptive and flexible two-scale coupling
Submitting author: @IshaanDesai
Handling editor: @philipcardiff (Active)
Reviewers: @mayrmt, @mrogowski, @mbkumar
Similarity score: 0.7349

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danielskatz]

@editorialbot assign @gkthiruvathukal as editor

Thanks @gkthiruvathukal

[editorialbot]

Assigned! @gkthiruvathukal is now the editor

[rohanbabbar04]

Thanks @gkthiruvathukal for taking this up

[gkthiruvathukal]

@rohanbabbar04
Can you let me know if you have any suggestions for potential reviewers? I am thinking of iljah and rainwoodman since they were involved in a similar JOSS submission where mpi4py was used.

[rohanbabbar04]

Hi @gkthiruvathukal,
Sure, you can ask iljah and rainwoodman if they are available, as I can see they have worked with mpi4py before. I can also look into potential reviewers to find more people.

[gkthiruvathukal]

@rohanbabbar04 I was thinking of these two as well!

[gkthiruvathukal]

@iljah and @rainwoodman, are you willing to help review this JOSS submission? I think it would be of interest, based on your past review for JOSS.

[rohanbabbar04]

Hi @gkthiruvathukal ,
It looks as if iljah and rainwoodman are not available at the moment, do you suggest we should look for more reviewers?

[rohanbabbar04]

Hi @gkthiruvathukal ,
Any update on this

[gkthiruvathukal]

@rohanbabbar04 Do you have any suggestions for more reviewers? I will be happy to reach out to them once you let me know. Sorry for the delay!

[rainwoodman]

Thanks for the invitation to be a reviewer. I have not been actively working with MPI and numerics for the last few years and in my present capacity I would not be in a good position to review this submission.

[rohanbabbar04]

Hi @gkthiruvathukal,

Here are a few suggestions for reviewers that I found from the list:

• Chilipp
• gonsie
• mikaem
• csadorf
• 1313e

Please feel free to suggest any additional reviewers who might be suitable for this project.

[rohanbabbar04]

Hi @gkthiruvathukal,
Do let me know if you need anything else from me
Thank You

[gkthiruvathukal]

@Chilipp and @gonsie Are you willing to help review this JOSS submission?

[Chilipp]

Thanks for asking @gkthiruvathukal but unfortunately I am not available for reviews for the rest of this year

[gkthiruvathukal]

@Chilipp Thanks for responding!

[gkthiruvathukal]

@gonsie and @mikaem Are you willing to help review this JOSS submission?

[mikaem]

Hi @gkthiruvathukal. It's been awhile since I contributed and this looks interesting, so count me in.

[gonsie]

yes, i am willing to review this submission.

[gkthiruvathukal]

@gonsie and @mikaem, thank you so much for your willingness to help! I will assign you now and start the review process.

[gkthiruvathukal]

@editorialbot add @gonsie as reviewer

[editorialbot]

@gonsie added to the reviewers list!

[gkthiruvathukal]

@editorialbot add @mikaem as reviewer

[editorialbot]

@mikaem added to the reviewers list!

[gkthiruvathukal]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7512.