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[REVIEW]: RHEA: an open-source Reproducible Hybrid-architecture flow solver Engineered for Academia #4637

Closed editorialbot closed 1 year ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@lluisjofre<!--end-author-handle-- (Lluis Jofre) Repository: https://gitlab.com/ProjectRHEA/flowsolverrhea Branch with paper.md (empty if default branch): master Version: v1.0.0 Editor: !--editor-->@diehlpk<!--end-editor-- Reviewers: @ctdegroot, @thomasgillis Archive: 10.5281/zenodo.7525886

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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 @ctdegroot

📝 Checklist for @thomasgillis

editorialbot commented 1 year ago

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:

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

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editorialbot commented 1 year ago 
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
editorialbot commented 1 year ago

Wordcount for paper.md is 1915

editorialbot commented 1 year ago 
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
editorialbot commented 1 year ago

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

thomasgillis commented 1 year ago

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

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?
thomasgillis commented 1 year ago

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:

code comments

ctdegroot commented 1 year ago

Review checklist for @ctdegroot

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

editorialbot commented 1 year ago

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

ctdegroot commented 1 year ago

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

I will continue my review once these items are addressed.

diehlpk commented 1 year ago

@lluisjofre please have a look into the comments above.

lluisjofre commented 1 year ago

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

diehlpk commented 1 year ago

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.

diehlpk commented 1 year ago

@lluisjofre just checking on the progress you made?

lluisjofre commented 1 year ago

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

diehlpk commented 1 year ago

Hi @ctdegroot, @thomasgillis could you please have a look at the comments above?

diehlpk commented 1 year ago

Reminder set for @ctdegroot in 2 weeks

diehlpk commented 1 year ago

Reminder set for @thomasgillis in 2 weeks

diehlpk commented 1 year ago

Hi @ctdegroot, @thomasgillis could you please have a look at the comments above?

diehlpk commented 1 year ago

Hi @ctdegroot, @thomasgillis could you please have a look at the comments above?

thomasgillis commented 1 year ago

Hi, thanks for the heads-up. I will look at this over the coming week

ctdegroot commented 1 year ago

Thanks, I will look at it in the next week as well.

diehlpk commented 1 year ago

Hi @ctdegroot, @thomasgillis could you please have a look at the comments above?

diehlpk commented 1 year ago

Hi @ctdegroot, @thomasgillis could you please have a look at the comments above?

diehlpk commented 1 year ago

Hi @ctdegroot, @thomasgillis could you please have a look at the comments above?

ctdegroot commented 1 year ago

I am working on this but the installation instructions are still very much lacking. It doesn't seem like this comment was addressed.

thomasgillis commented 1 year ago

Review checklist for @thomasgillis

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

thomasgillis commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

thomasgillis commented 1 year ago

Thanks for the updated version of the software as well as the work put in it. Here is a list of the additional comments I have. Let me know if you have further questions

general comments


// https://gitlab.com/ProjectRHEA/flowsolverrhea/-/blob/master/src/ParallelTimer.cpp#L34
// function stop()
MPI_Barrier(MPI_COMM_WORLD);
time_array[str][1] = getTime_cpu();
time_array[str][2] = time_array[str][1] - time_array[str][0];      
// [...]
ltime = time_array[str][2];
MPI_Allreduce(&ltime,&maxtime,1,MPI_DOUBLE,MPI_MAX,MPI_COMM_WORLD);
MPI_Allreduce(&ltime,&mintime,1,MPI_DOUBLE,MPI_MIN,MPI_COMM_WORLD);
MPI_Allreduce(&ltime,&avgtime,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);

Fig1: this figure is still very puzzling to me. I don't fully understand what you did: which testcase, how many unknowns per rank, which time-integration, etc. Additionally:

more subjective comments

diehlpk commented 1 year ago

@lluisjofre can you please have a look?

diehlpk commented 1 year ago

@lluisjofre can you please have a look?

lluisjofre commented 1 year ago

Dear @diehlpk,

We have completed answering the comments/questions raised by the 2 reviewers. Responses are available in the PDF files attached to this message. The git repository has been correspondingly updated.

Thanks for your time and attention.

Best, Lluis

response_ctdegroot.pdf response_thomasgillis.pdf

diehlpk commented 1 year ago

@ctdegroot can you please have a look?

diehlpk commented 1 year ago

@thomasgillis can you please have a look?

thomasgillis commented 1 year ago

thanks for the update (and the time spent on it!). I still have one comment on the scalability claim, the rest looks good to me.

As previously explained I disagree on the assertion "the solver presents similar speedups in terms of strong scalability when running on CPUs and CPUs+GPUs". Scalability is independent from the speed as it's a ratio of time-to-solution. instead scalability comes from the percentage of your program that can be run in parallel. From the figures, we can roughly estimate that at a ratio of 32 the speedup is

lluisjofre commented 1 year ago

Dear @thomasgillis and @diehlpk,

We agree with your comment @thomasgillis. We have subsequently modified the manuscript as: "Second, as shown in Figure 1, on BSC for a fixed-problem size and noting that on CPUs+GPUs the solver is roughly faster, the solver presents strong scalability speedups above 80% and 60%, respectively, when running on CPUs and CPUs+GPUs up to 32 nodes (640 cores and 128 GPUs)." The git repository has been correspondingly updated.

Thanks for your time and attention.

Best, Lluis

diehlpk commented 1 year ago

@thomasgillis does this satisfy you?

thomasgillis commented 1 year ago

@thomasgillis does this satisfy you? yes, thank you

diehlpk commented 1 year ago

@thomasgillis Can you please have a look at your check list. There are some unchecked boxes.

diehlpk commented 1 year ago

@thomasgillis Can you please have a look at your check list. There are some unchecked boxes.

diehlpk commented 1 year ago

@editorialbot generate pdf

diehlpk commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

diehlpk commented 1 year ago

@editorialbot check references

diehlpk commented 1 year ago

@ctdegroot How is your review going?

editorialbot commented 1 year ago 
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
- 10.1063/1.3676783 may be a valid DOI for title: Grid-point requirements for large eddy simulation: Chapman’s estimates revisited
- 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
- Errored finding suggestions for "Riemann Solvers and Numerical Methods for Fluid Dy...", please try later

INVALID DOIs

- None
editorialbot commented 1 year ago 
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
- 10.1063/1.3676783 may be a valid DOI for title: Grid-point requirements for large eddy simulation: Chapman’s estimates revisited
- 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
- Errored finding suggestions for "HTR solver: an open-source Exascale-oriented task-...", please try later
- 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
diehlpk commented 1 year ago

@lluisjofre please add all the missing DOIs to the paper.

diehlpk commented 1 year ago

@ctdegroot How is your review going?