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

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@j6hickey@nicoguaro<!--end-editor-- Reviewers: @dortiz5, @chennachaos Archive: Pending 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 commented 3 months ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 1995

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

🔴 Failed to discover a valid open source license

editorialbot commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

nicoguaro commented 3 months ago

@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 commented 3 months ago

@nicoguaro done. Thanks!

nicoguaro commented 3 months ago

@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 commented 3 months ago

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

chennachaos commented 3 months ago

Review checklist for @chennachaos

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source for this learning module available at the https://github.com/ARC4CFD/arc4cfd.github.io?
[x] 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)
[x] Version: Does the release version given match the repository release?
[x] 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

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] 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 commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

@editorialbot commands

chennachaos commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

chennachaos commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

Thanks for the clarification, @j6hickey!

nicoguaro commented 2 months ago

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

dortiz5 commented 2 months ago

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 commented 2 months ago

Review checklist for @dortiz5

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source for this learning module available at the https://github.com/ARC4CFD/arc4cfd.github.io?
[x] 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)
[x] Version: Does the release version given match the repository release?
[x] Authorship: Has the submitting author (@j6hickey) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
[x] 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!)

[x] 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.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
[x] 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

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

dortiz5 commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

dortiz5 commented 2 months ago

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 commented 1 month ago

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 commented 1 month ago

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 commented 1 month ago

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

j6hickey commented 1 week ago

@nicoguaro @chennachaos I was wondering if there were any updates on the proposed revisions needed for this manuscript. Thanks for all your help!

Best, Jean-Pierre

chennachaos commented 2 days ago

Hi @j6hickey. I was occupied with too many reviews from the other journals and missed this one. I will have my comments by the end of the week.

openjournals / jose-reviews