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

whedon commented 4 years ago

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

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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:

Make sure you're logged in to your GitHub account
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

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 4 years ago

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 :tada:.

:star: Important :star:

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:

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

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

@whedon generate pdf

whedon commented 4 years ago

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

Can't find any papers to compile :-(

ali-ramadhan commented 4 years ago

@whedon generate pdf from branch joss-paper

whedon commented 4 years ago

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

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

ali-ramadhan commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

@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 commented 4 years ago

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

ali-ramadhan commented 4 years ago

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:

kthyng commented 4 years ago

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

danielskatz commented 4 years ago

@whedon re-invite @ysimillides as reviewer

whedon commented 4 years ago

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

danielskatz commented 4 years ago

👋 @arfon - can you explain this?

arfon commented 4 years ago

@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 commented 4 years ago

OK, errors should be more semantic now as of https://github.com/openjournals/whedon-api/pull/94

ysimillides commented 4 years ago

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

arfon commented 4 years ago

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 commented 4 years ago

@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 commented 4 years ago

Hi everyone! We are officially starting JOSS back up today. We know that everyone has different circumstances with work and home life right now, so we want to figure out a way forward that will work for everyone.

@ysimillides — are you still able to review this submission? If so, what timeline would work for you?

ysimillides commented 4 years ago

Hello, I can't access the checklist above, but by going through the items my main concern is that there is no comparison / mention of other similar software which can be found ( state of the field on the checklist). If a few lines in the paper could be added to reflect this, that would be ideal ( and likewise if their are no similar packages, this should be explicitly stated).

Otherwise everything seems fine and the package follows best practices for Julia packages ( integrated with the package manager, automated tests +documentation )

arfon commented 4 years ago

@whedon re-invite @ysimillides as reviewer

whedon commented 4 years ago

The reviewer already has a pending invite.

@ysimillides please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

arfon commented 4 years ago

@ysimillides - it sounds like you might need to accept the invite above to the repository - this will allow you to update the checklist above.

kthyng commented 4 years ago

Hi @ysimillides! Were you able to accept the invitation above to gain permissions for your checklist? Have you been able to install the software and try it out?

kthyng commented 4 years ago

Hi @ysimillides — will you be able to work on this review? Everything is in disarray right now so it's totally understandable if you won't be able to finish it, but in that case please do let me know so we can get a new reviewer.

kthyng commented 4 years ago

Note for reference: just reached out to @ysimillides by email to confirm.

kthyng commented 4 years ago

@ali-ramadhan I'm sorry about the delay on reviewing your submission. I am going to remove the delinquent reviewer and find another to replace so we can finally move forward.

kthyng commented 4 years ago

@whedon remove @ysimillides as reviewer

whedon commented 4 years ago

OK, @ysimillides is no longer a reviewer

kthyng commented 4 years ago

@mancellin — would you be interested in reviewing this submission to JOSS? We already have one review completed but the other reviewer went MIA. You look like a good reviewer knowing Julia and related CFD.

mancellin commented 4 years ago

Sure, I can do that. It looks like an interesting work.

kthyng commented 4 years ago

@mancellin awesome! Thank you!!

kthyng commented 4 years ago

@whedon add @mancellin as reviewer

whedon commented 4 years ago

OK, @mancellin is now a reviewer

kthyng commented 4 years ago

@mancellin You should be good to go, but let me know if you have any permissions problems or questions. Thank you!

ali-ramadhan commented 4 years ago

@kthyng No worries about the delay, thank you for keeping this review moving forward!

I've fallen off the grid in the past few months myself but I believe we've addressed most of the points from @funsim's review so I'll reply more formally to the review soon.

@mancellin Thanks so much for agreeing to review our submission! Please let me know if you hit any issues or have any questions.

kthyng commented 4 years ago

@mancellin just a friendly reminder about this review. When might you be able to work on this? Thanks again.

mancellin commented 4 years ago

@kthyng Thank you for the reminder. I've started working on the review. I plan to complete it after some more tests in one or two weeks.

mancellin commented 4 years ago

Overall, this is a very nice package. The documentation is extensive, the package is easy to install and works as expected.

I have some issues running simulations on GPU, but I believe it to be due to my own setup and not to the package itself. I'll give it another try in the next days and open an issue if I need help.

One minor issue (already mentioned by @ysimillides): the review check-list requires the authors to compare their code to other commonly-used packages. Could you add a few lines in the paper about the state of the art, citing other simulation codes targetting the same problem (if they exist)?

Besides, have the minor issues raised by @funsim in January been addressed?

ali-ramadhan commented 4 years ago

Thank you for the review and the kind words @mancellin!

I have some issues running simulations on GPU, but I believe it to be due to my own setup and not to the package itself. I'll give it another try in the next days and open an issue if I need help.

Apologies about this. We discovered a major bug concerning running GPU simulations that we fixed in Oceananigans v0.32.0 last week, so maybe try a more recent version if you were trying an older one. Otherwise we'd love to hear more about the issue so we can fix it.

One minor issue (already mentioned by @ysimillides): the review check-list requires the authors to compare their code to other commonly-used packages. Could you add a few lines in the paper about the state of the art, citing other simulation codes targetting the same problem (if they exist)?

Thank you for bringing this up. I will update the software paper with a discussion of other similar packages.

Besides, have the minor issues raised by @funsim in January been addressed?

Yes I believe so (the issues have been closed) but I think I still need to post a formal reply. Sorry about this delay on my part. I will do it today.

ali-ramadhan commented 4 years ago

@whedon generate pdf from branch joss-paper

whedon commented 4 years ago

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

whedon commented 4 years ago

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

Error reading bibliography ./paper.bib (line 64, column 3): unexpected "y" expecting space, ",", white space or "}" Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

ali-ramadhan commented 4 years ago

@whedon generate pdf from branch joss-paper

whedon commented 4 years ago

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

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

ali-ramadhan commented 4 years ago

@whedon generate pdf from branch joss-paper

whedon commented 4 years ago

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

openjournals / joss-reviews