joss-reviews [REVIEW]: RHEA: an open-source Reproducible Hybrid-architecture flow solver Engineered for Academia

Submitting author: @lluisjofre (Lluis Jofre) Repository: https://gitlab.com/ProjectRHEA/flowsolverrhea Branch with paper.md (empty if default branch): master Version: v1.0.0 Editor: @diehlpk Reviewers: @ctdegroot, @thomasgillis Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/23f32f49c31a2e3debb495234a64e4e8"><img src="https://joss.theoj.org/papers/23f32f49c31a2e3debb495234a64e4e8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/23f32f49c31a2e3debb495234a64e4e8/status.svg)](https://joss.theoj.org/papers/23f32f49c31a2e3debb495234a64e4e8)

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

@ctdegroot & @thomasgillis, 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://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @diehlpk 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 @thomasgillis

📝 Checklist for @ctdegroot

Aug 02 '22 15:08 editorialbot

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

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

@editorialbot commands

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

@editorialbot generate pdf

Aug 02 '22 15:08 editorialbot

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (581.4 files/s, 179243.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             21           2259           2095           8546
Python                          10            302            467           1426
C/C++ Header                    14            552            582           1039
YAML                            11            139            400            932
TeX                              1              0              0            220
Markdown                         2             25              0             66
make                             2             14             12             37
Bourne Shell                     1              0              1              1
-------------------------------------------------------------------------------
SUM:                            62           3291           3557          12267
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

Aug 02 '22 15:08 editorialbot

Wordcount for paper.md is 1915

Aug 02 '22 15:08 editorialbot

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

OK DOIs

- None

MISSING DOIs

- 10.1115/1.4054554 may be a valid DOI for title: Thermophysical analysis of microconfined turbulent flow regimes at supercritical fluid conditions in heat transfer applications
- 10.1016/j.jcp.2019.01.007 may be a valid DOI for title: Numerically stable formulations of convective terms for turbulent compressible flows
- 10.1137/s003614450036757x may be a valid DOI for title: Strong stability-preserving high-order time discretization methods
- 10.1109/mcse.2013.47 may be a valid DOI for title: Survey of multiscale and multiphysics applications and communities
- 10.1016/j.cpc.2020.107262 may be a valid DOI for title: HTR solver: an open-source Exascale-oriented task-based multi-GPU high-order code for hypersonic aerothermodynamics
- 10.1016/j.pecs.2020.100877 may be a valid DOI for title: Transcritical diffuse-interface hydrodynamics of propellants in high-pressure combustors of chemical propulsion systems
- 10.1007/s00158-022-03293-y may be a valid DOI for title: Rapid aerodynamic shape optimization under uncertainty using a stochastic gradient approach
- 10.1063/1.869966 may be a valid DOI for title: Direct numerical simulation of turbulent channel flow up to Re_τ=590
- 10.1146/annurev.fluid.010908.165248 may be a valid DOI for title: Uncertainty quantification and polynomial chaos techniques in computational fluid dynamics
- 10.1016/j.jocs.2016.11.001 may be a valid DOI for title: OpenSBLI: a framework for the automated derivation and parallel execution of finite difference solvers on a range of computer architectures
- 10.1109/tim.2022.3165790 may be a valid DOI for title: Superheterodyne microwave system for the detection of bioparticles with coplanar electrodes on a microfluidic platform
- 10.1016/0021-9991(92)90227-p may be a valid DOI for title: Boundary conditions for direct simulations of compressible viscous flows
- 10.1016/j.cpc.2021.107906 may be a valid DOI for title: STREAmS: a high-fidelity accelerated solver for direct numerical simulation of compressible turbulent flows

INVALID DOIs

- None

Aug 02 '22 15:08 editorialbot

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

Aug 02 '22 15:08 editorialbot

Old list and needs to be ignored.

Review checklist for @thomasgillis

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 https://gitlab.com/ProjectRHEA/flowsolverrhea?

[x] 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 (@lluisjofre) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?

[ ] 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?

Aug 02 '22 15:08 thomasgillis

Thanks for your work in the software @lluisjofre, here is a list of my comments. I don't think I have access to your issues, so couldn't open a new one on the target repo :-)

paper comment

The paper is 1900 words while the limit is at 1000, maybe you will want to reduce it. There are plenty of non-relevant details that could go away and you might want to tighten your english a bit more. I would definitely rewrite your sections summary, statement of the need, etc. to make them more explicit about what you do and others do or don't.

I also have specific questions:

you claim to be open-source and reproducible, what makes the code more reproducible than others? What does it mean to you to be reproducible?
your relationships between N and Re should either be detailed or refer to a citation (and I have N ~ Re^3 in mind).
Your figure 1 (left) is very unclear to me. "First, when 100 using CPUs+GPUs with respect to only CPUs, the solver is accelerated approximately 2.5× 101 and 5× on the Hybrid and BSC computers" where do you see that, I only see time and energy.
please add a weak analysis and some sense of the percentage of parallel regions in your program (can be numerically estimated from both the strong and weak scaling). the sentence "the solver presents nearly ideal speedup" is very subjective.
Although 32 nodes is nice, the rank count is very low (<1000) and contrasts with your claim "mid-size workstations to the largest supercomputers worldwide". I think that any recent MPI implementations will have no problems to scale up to 600 ranks. Any chance you can get above 4k to present a more accurate picture?

code comments

it's difficult to verify your authorship as the contributions on gitlab come from the same user "ProjectRHEA" and you are not recognized as an author on gitlab. Any way to fix that?
you don't have any automated documentation in the code for the most part of the classes I could visit. it makes the software very difficult to understand as well as difficult to maintain.
you don't have any CI/CD pipeline on gitlab
I randomly checked your code and you have sometimes weird coding practices like using namespace std; in headers or enforcing a MPI_Barrier before stopping a timer.

Aug 02 '22 17:08 thomasgillis

Review checklist for @ctdegroot

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 https://gitlab.com/ProjectRHEA/flowsolverrhea?
[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 (@lluisjofre) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[ ] 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?

Aug 03 '22 19:08 ctdegroot

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

Aug 03 '22 19:08 editorialbot

Some preliminary comments on the code before I get it installed.

Installation instructions are lacking. I don't have YAML installed and there are no instructions or link about how to install it or what version I need. The instruction to "Modify Makefile (paths & flags) according to the computing system" is not great. This needs to be improved.
There is no apparent documentation for example usage. There are some cases tucked into the "tests" directory but no instructions what to do with them.
I opened some files at random and did not see much documentation of the software API. For example, the class ManagerHDF, there is absolutely no documentation about what this does or how to use it. It does not seem to meet the requirements for "Functionality documentation" described above.
Integration tests do not seem to automated and there are no instructions how to run them. I don't see any unit tests to document functionality of various functions/classes.
There are no guidelines for how to contribute to the software, report issues, or seek support.

I will continue my review once these items are addressed.

Aug 03 '22 20:08 ctdegroot

@lluisjofre please have a look into the comments above.

Aug 09 '22 19:08 diehlpk

Dear @diehlpk,

Thanks for organizing the review. We have started making modifications to the paper and code following the indications from the reviewers. How much time do we have to make the modifications?

Thanks for your time and attention.

Best, Lluis

Aug 13 '22 18:08 lluisjofre

Dear @diehlpk,

Thanks for organizing the review. We have started making modifications to the paper and code following the indications from the reviewers. How much time do we have to make the modifications?

Thanks for your time and attention.

Best, Lluis

@lluisjofre you are welcome. I do not have a strict schedule yet. However, if you could address all the issues within 6 weeks would be good. I would appreciate if you report any progress here, so the reviewers could look at them.

Aug 14 '22 00:08 diehlpk

@lluisjofre just checking on the progress you made?

Sep 01 '22 22:09 diehlpk

Dear @diehlpk,

We have completed answering the comments/questions raised by the 2 reviewers. Responses are available in the PDF file attached to this message.

Thanks for your time and attention.

Best, Lluis response_to_reviewers_4637.pdf

Sep 03 '22 09:09 lluisjofre