[REVIEW]: Oceananigans.jl: Fast and friendly geophysical fluid dynamics on GPUs

[whedon]

Submitting author: @ali-ramadhan (Ali Ramadhan)
Repository: https://github.com/CliMA/Oceananigans.jl
Version: v0.36.0
Editor: @kthyng
Reviewers: @funsim, @mancellin
Archive: 10.5281/zenodo.4019272

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/aeb75d5b99d40ae6e0c8a3a4f09f3285"><img src="https://joss.theoj.org/papers/aeb75d5b99d40ae6e0c8a3a4f09f3285/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/aeb75d5b99d40ae6e0c8a3a4f09f3285/status.svg)](https://joss.theoj.org/papers/aeb75d5b99d40ae6e0c8a3a4f09f3285)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@funsim & @mancellin, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @kthyng know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @funsim

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@ali-ramadhan) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @mancellin

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@ali-ramadhan) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @funsim, @ysimillides it looks like you're currently assigned to review this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2018 with the following error:

Can't find any papers to compile :-(

[ali-ramadhan]

@whedon generate pdf from branch joss-paper

[whedon]

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[ali-ramadhan]

Thanks so much @funsim and @ysimillides for agreeing to review our submission!

Please let me know if you guys need access to GPUs and we can figure something out.

[whedon]

Reference check summary:

OK DOIs

- 10.1029/96JC02775 is OK
- 10/f9wkpj is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5670/oceanog.2016.66 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[funsim]

Overall this software package is very well set up and I recommend the submission to be accepted by JOSS after addressing the following comments:

Software paper
I cannot find the software paper - could you please send me a link?

Performance

• The performance plots on the README.md file show that the single precision speed up for CPUs is below 1. This is surprising and should be commented on.
• The link to benchmarks.jl in the README.md file is broken.

Functionality documentation

• Citation commands are not working in documentation page:
  https://climate-machine.github.io/Oceananigans.jl/stable/numerical_implementation/large_eddy_simulation/
• I suggest to link the API documentation with the mathematical description. For instance, you could mention the Julia commands when describing the numerical handling of boundary conditions in https://climate-machine.github.io/Oceananigans.jl/stable/numerical_implementation/boundary_conditions/

Functionality:

• It seems that you have not performed a convergence test of your numerical model (based on analytical known solutions or manufactured solutions). I suggest that you add this (for instance based on the Taylor Green example)

I would like to thank @jakobes for helping me in this review.

[kthyng]

@funsim You can find the paper above by clicking "check article proof"

Please note, for both @funsim and @ali-ramadhan: if there will be more discussion on the points noted above, it's preferable to have that discussion in individual issues that are opened and linked to this review issue. That way this issue remains more of an overview and details can be hashed out elsewhere. Thanks!

[funsim]

Found the paper, thanks. Apart from the comments above, I have no further comments.

[ali-ramadhan]

Thank you @funsim for the quick review! You bring up good points that will improve the package. Certainly the documentation needs more work as you've pointed out, and we've been meaning to add a verification experiment with some convergence results so thank you for bringing it up.

I have opened an issue for each of your comments where we will work towards addressing them:

1. Update performance benchmarks plot and discuss results CliMA/Oceananigans.jl#607
2. Update README and fix broken links CliMA/Oceananigans.jl#608
3. Fix citations and references in documentation CliMA/Oceananigans.jl#609
4. Link documentation of numerical methods with code and API CliMA/Oceananigans.jl#610
5. Taylor-Green vortex verification experiment and convergence test CliMA/Oceananigans.jl#611

[kthyng]

Hi @ysimillides! When do you think you'll be able to work on your review?

[danielskatz]

@whedon re-invite @ysimillides as reviewer

[whedon]

Sorry, I couldn't re-invite @ysimillides.

[danielskatz]

👋 @arfon - can you explain this?

[arfon]

@danielskatz - I think this is because they have already been invited (I can see a pending invite on the repository). I don't think GitHub gives us any kind of semantic response when issuing these invites.

[arfon]

OK, errors should be more semantic now as of openjournals/whedon-api#94

[ysimillides]

Apologies for the delay, will try and get it done by the end of this week!

[arfon]

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

[kthyng]

@ysimillides Everyone's situation is totally different, so not sure if you have any time for work right now, but if you do, we'd appreciate hearing from you on this review at some point. Thank you.

[kthyng]

@whedon generate pdf

[whedon]

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

[kthyng]

@openjournals/dev Could you see why I can generate the paper but not accept it? Thank you.

[arfon]

I think Whedon is struggling with an unusual DOI. This PR should fix the issue: CliMA/Oceananigans.jl#966

[ali-ramadhan]

Thank you @arfon! Just merged CliMA/Oceananigans.jl#966. Not sure where I got the old DOI from...

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1029/96JC02775 is OK
- 10.1137/141000671 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5670/oceanog.2016.66 is OK
- 10.1029/2019MS001726 is OK
- 10.1103/PhysRevResearch.2.023068 is OK
- 10.5194/gmd-13-1335-2020 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1743

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1743, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@kthyng - I'm not sure if you had other checks to make here but this paper is now compiling properly.

[kthyng]

@arfon thank you. I didn't even look at the DOIs, just saw that they were listed as ok and ignored them. Thanks.

[kthyng]

@ali-ramadhan Ok great! You are developing quickly. Do you want to use your now newest version in this publication or stop at v0.36? Also can you change the metadata in the JOSS zenodo archive so that the title and author list exactly match your JOSS paper?

[ali-ramadhan]

@kthyng Ah I think we'll stick with v0.36.0 here as we specifically tagged it for JOSS (if that's okay with JOSS).

I thought I did change the JOSS Zenodo archive metadata for v0.36.0 so the authors match the JOSS paper authors exactly (https://zenodo.org/record/4019272 from #2018 (comment)).

There is a newer different Zenodo entry for v0.37.0 that pulled the authors from GitHub contributors. I can change the authors on this Zenodo archive as well if needed?

[kthyng]

@kthyng Ah I think we'll stick with v0.36.0 here as we specifically tagged it for JOSS (if that's okay with JOSS).

No problem!

I thought I did change the JOSS Zenodo archive metadata for v0.36.0 so the authors match the JOSS paper authors exactly (https://zenodo.org/record/4019272 from #2018 (comment)).

The title at that link is "CliMA/Oceananigans.jl: v0.36.0" but your submission title is "Oceananigans.jl: Fast and friendly geophysical fluid dynamics on GPUs". Author list looks fine on a quick glance.

[ali-ramadhan]

Ah sorry I misread your comment! Just updated the title so I think both title and author list at https://zenodo.org/record/4019272 should match now.

[kthyng]

Excellent! That is everything now. Sorry that this has been a slow process, but appreciate you sticking with us through an on-going global pandemic.

[kthyng]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02018 joss-papers#1744
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02018
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congrats to @ali-ramadhan on your new publication! Many thanks to reviewers @funsim and @mancellin. Without your hard work and expertise we wouldn't be able to do this process. 🎉 🎉

(I will leave this issue open until the doi resolves)

[ali-ramadhan]

Awesome! Thanks so much @kthyng, @funsim, and @mancellin for your helpful reviews and feedback.

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02018/status.svg)](https://doi.org/10.21105/joss.02018)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02018">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02018/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02018/status.svg
   :target: https://doi.org/10.21105/joss.02018

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss