[REVIEW]: ARC4CFD: Learning how to leverage High-Performance Computing with Computational Fluid Dynamics

[editorialbot]

Submitting author: @j6hickey (Jean-Pierre Hickey)
Repository: https://github.com/ARC4CFD/arc4cfd.github.io
Branch with paper.md (empty if default branch):
Version: 1.0.0
Editor: @nicoguaro
Reviewers: @dortiz5, @chennachaos
Archive: 10.5281/zenodo.14340786
Paper kind: learning module

Status

Status badge code:

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Markdown: [![status](https://jose.theoj.org/papers/3e91be78e941500c610404abf281a734/status.svg)](https://jose.theoj.org/papers/3e91be78e941500c610404abf281a734)

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

@dortiz5 & @chennachaos, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://openjournals.readthedocs.io/en/jose/reviewer_guidelines.html. Any questions/concerns please let @nicoguaro know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @chennachaos

📝 Checklist for @dortiz5

[editorialbot]

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[editorialbot]

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

OK DOIs

- 10.21105/jose.00021 is OK

MISSING DOIs

- No DOI given, and none found for title: High-performance computing in computational fluid ...

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.19 s (545.3 files/s, 317743.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                             58            397             79          42977
JSON                             3              0              0           9015
Markdown                        32           1747              0           4410
TeX                              3             89              0           1097
XML                              1              1              1            258
CSS                              1             43              8            247
YAML                             2              9             14             90
JavaScript                       1              3             11             87
TypeScript                       3              1              2             15
-------------------------------------------------------------------------------
SUM:                           104           2290            115          58196
-------------------------------------------------------------------------------

Commit count by author:

   263	Jean-Pierre Hickey
    90	FrancescoAmbrogi
    27	Sophie Hillcoat
     8	srhillco
     6	Sophie
     4	ARC4CFD
     3	j6hickey
     1	shillcoat

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1995

✅ 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 📄 👈

[nicoguaro]

@j6hickey, could you please add a license to the repository so we can proceed with the review?

License info:

🔴 Failed to discover a valid open source license

[j6hickey]

@nicoguaro done. Thanks!

[nicoguaro]

@dortiz5, @chennachaos, this is the space where the review process takes form. There is a checklist for each one, tick the boxes when you see that the criterion is satisfied. You can generate the checklist with

@editorialbot generate my checklist

I will be here to answer the questions that you might have.

Let us use as a tentative timeframe the last week of Augist, is that OK for you?

[chennachaos]

Thanks, @nicoguaro! I will follow it up here.

[chennachaos]

Review checklist for @chennachaos

Conflict of interest

• As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

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

General checks

• Repository: Is the source for this learning module available at the https://github.com/ARC4CFD/arc4cfd.github.io?
• License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
• Version: Does the release version given match the repository release?
• Authorship: Has the submitting author (@j6hickey) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• Installation instructions: Is there a clearly stated list of dependencies?
• Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

• Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
• Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Does the paper clearly state the need for this module and who the target audience is?
• Description: Does the paper describe the learning materials and sequence?
• Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
• Could someone else teach with this module, given the right expertise?
• Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[chennachaos]

@editorialbot generate pdf

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[chennachaos]

@editorialbot generate pdf

[editorialbot]

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

[chennachaos]

Hi @nicoguaro, Regarding authorship, the submitting author, @j6hickey, made only 3 out of 431 commits. Is this contribution sufficient? Are there any guidelines on the amount of contribution by the submitting author?

[j6hickey]

Hi @chennachaos and @nicoguaro, to clarify this point, most of the submissions on this work were done from the @mpilab-uw account which is the git account I use for the lab.

[chennachaos]

Thanks for the clarification, @j6hickey!

[nicoguaro]

@dortiz5, is there something that we can do to help you start with this review?

[dortiz5]

Dear all, I apologize for the delay. I have been overloaded with work this month. I will be working on the revision this week and hope to finish it before the weekend.

[dortiz5]

Review checklist for @dortiz5

Conflict of interest

• As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

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

General checks

• Repository: Is the source for this learning module available at the https://github.com/ARC4CFD/arc4cfd.github.io?
• License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
• Version: Does the release version given match the repository release?
• Authorship: Has the submitting author (@j6hickey) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• Installation instructions: Is there a clearly stated list of dependencies?
• Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

• Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
• Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Does the paper clearly state the need for this module and who the target audience is?
• Description: Does the paper describe the learning materials and sequence?
• Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
• Could someone else teach with this module, given the right expertise?
• Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[dortiz5]

@editorialbot generate pdf

[editorialbot]

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

[dortiz5]

Dear @j6hickey, thank you for this fantastic course and the related repository.
The course has different learning sections with examples, nice images, explanatory videos, quizzes, and a glossary. Also, it was very interesting, pedagogical, and self-contained. More precisely, I found section 2 very beneficial to reduce the gap between small-scale and large-scale simulations, which is the main scope of the course.
I have some suggestions regarding the checklist:
1- Including a version indicator of the course would be helpful if further relevant changes are made.
2- Although the course is self-contained, it would be beneficial for students and other instructors to include a brief description in the documentation of the repository of the programs and packages in Windows, Mac, and Linux to be used during the course. Also, include the recommended minimal version to ensure the best experience and avoid further problems.
3- Finally, include brief instructions in the repository's documentation on making third-party contributions, such as including the link (https://arc4cfd.github.io/contact/) to send you the comments.
Best regards,
David

[j6hickey]

We would like to thank @dortiz5 for the wonderful feedback that was provided. We have addressed all the suggestions that helped to strengthen the course. Here are some details on what was done:
1- We included a version tracker into the git repository. This will allow the course authors to flag any major changes to the course content. At the moment, as the course is on its first release, we have set the version counter to V1.0.
2- This was a very good point. We designed the course for users of the Digital Research Alliance of Canada clusters which share a common software stack. As the course was also intended for non-Canadian users and users without access to HPC, we have added a discussion in the Overview page about these points. We also clarified the versions of the open-source toolkit used in the course (namely Gmsh, OpenFoam, and SU2) as well as the minimal version requirement for the installation of the codes. We have also referred the learners back to this page if they want to install these tools locally.
3 – We have added a short description in the Overview about how the community can contribute to this on-going course development. It is intended that a synchronous version of this course will be offered yearly in June as part of the Compute Ontario Summer School, therefore any changes and improvements will likely occurs around this time of year.

[nicoguaro]

I am checking on the advance of this review.

• @dortiz5, do you consider that the changes made address your comments?

• @chennachaos, do you have any updates from your end?

[dortiz5]

@nicoguaro, yes, it looks nicely done for me.
Best regards,
David

[editorialbot]

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

[nicoguaro]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.20 s (512.6 files/s, 297918.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                             59            398             80          43333
JSON                             3              0              0           9015
Markdown                        32           1754              0           4419
TeX                              3             93              0           1138
XML                              1              1              1            258
CSS                              1             43              8            247
YAML                             2              9             14             90
JavaScript                       1              3             11             87
TypeScript                       3              1              2             15
-------------------------------------------------------------------------------
SUM:                           105           2302            116          58602
-------------------------------------------------------------------------------

Commit count by author:

   271	Jean-Pierre Hickey
    90	FrancescoAmbrogi
    27	Sophie Hillcoat
     8	srhillco
     6	ARC4CFD
     6	JPH
     6	Sophie
     3	j6hickey
     1	shillcoat

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2155

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[nicoguaro]

@j6hickey, I think that your work would benefit of using two licenses, one for the code (it might be MIT) and the one you are already using CC4-NC-SA. What do you think?

[j6hickey]

@nicoguaro Thanks. Good idea. We added the MIT licence to cover the software side of the work.

[nicoguaro]

@editorialbot generate pdf

[editorialbot]

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

[nicoguaro]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.19 s (546.5 files/s, 317567.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                             59            398             80          43333
JSON                             3              0              0           9015
Markdown                        32           1754              0           4419
TeX                              3             93              0           1138
XML                              1              1              1            258
CSS                              1             43              8            247
YAML                             2              9             14             90
JavaScript                       1              3             11             87
TypeScript                       3              1              2             15
-------------------------------------------------------------------------------
SUM:                           105           2302            116          58602
-------------------------------------------------------------------------------

Commit count by author:

   272	Jean-Pierre Hickey
    90	FrancescoAmbrogi
    27	Sophie Hillcoat
     8	srhillco
     6	ARC4CFD
     6	JPH
     6	Sophie
     3	j6hickey
     1	shillcoat

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2155

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[nicoguaro]

@j6hickey can you create a new version of the repo and archive it at Zenodo?

[j6hickey]

Yes, I have uploaded to Zenodo. To finalize the archival process, I would need the DOI and other information on the paper. Here is the DOI of the Zenodo repository: https://doi.org/10.5281/zenodo.14340786

[nicoguaro]

@editorialbot generate pdf

[editorialbot]

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

[nicoguaro]

@editorialbot set https://doi.org/10.5281/zenodo.14340786 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.14340786

[nicoguaro]

@editorialbot generate pdf

[editorialbot]

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

[nicoguaro]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

✅ OK DOIs

- 10.21105/jose.00021 is OK
- 10.1098/rsta.2002.0990 is OK
- 10.1002/nme.2579 is OK
- 10.1063/1.168744 is OK
- 10.2514/6.2013-287 is OK
- 10.1016/b978-012387582-2/50038-1 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/jose-papers#161, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[nicoguaro]

@labarba, this paper is ready to move forward.

[labarba]

I found the paper to be a little verbose in places, and when running into a couple of actual typos decided to go back and do a little copy editing. See my PR here:
ARC4CFD/arc4cfd.github.io#2

[labarba]

License mismatch: the Zenodo repository shows a Creative Commons Attribution Non Commercial 4.0 International, but elsewhere it is shown as CC BY NC SA.

While I mention that, may I raise a question about your choice of a non-commercial license? There are a few reasons why this could be problematic. See: https://gw-ospo.github.io/oss-licensing/license_your_own_work.html#empowering-others-to-build-upon-your-work

[j6hickey]

Thanks for the comments on the repository. We were unaware of the potential issues arising from the non-commercial licence. We have decided to use a CC BY 4.0 licence instead. These changes have now been applied to the git repo and a new version of the repository was uploaded to the zenodo archive: https://doi.org/10.5281/zenodo.14593527. These changes should address the licence mismatch concern.