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

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@lluisjofre@diehlpk<!--end-editor-- Reviewers: @ctdegroot, @thomasgillis Archive: 10.5281/zenodo.7525886

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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

@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

lluisjofre commented 1 year ago

Dear @diehlpk,

We have added all the DOIs (available) to the paper. The new version of the manuscript is available on the git repository.

Best, Lluis

diehlpk commented 1 year ago

@ctdegroot how is your review going?

ctdegroot commented 1 year ago

The installation instructions have improved, but "Adapt Makefile (compiler, flags & paths: CXX, CXXFLAGS, LDFLAGS, INC_LIB_YAML, INC_DIR_YAML, INC_LIB_HDF5, INC_DIR_HDF5) to the computing system" is not particularly helpful if the user is not a proficient Linux user. Perhaps the authors could provide default paths for these items or some suggestions about how to set them correctly. At the very least, what headers are these supposed to point to so the user can find them? What flags are typical to set for CXXFLAGS and LDFLAGS and what is their purpose?

lluisjofre commented 1 year ago

Dear @ctdegroot and @diehlpk,

Thanks a lot for the comments. We have improved the README.md file of the project following your instructions. In particular, the INSTALLATION instructions have been modified to: Adapt Makefile (flags & paths: CXXFLAGS, INC_LIB_YAML, INC_DIR_YAML, INC_LIB_HDF5, INC_DIR_HDF5) to the computing system. Examples:

CPU flags: CXXFLAGS = -O3 -Wall -std=c++0x -Wno-unknown-pragmas -Wno-unused-variable -I$(PROJECT_PATH)
CPU-GPU flags with managed OpenACC: CXXFLAGS = -fast -acc -ta=tesla:managed -Minfo=accel -O3 -Wall -std=c++0x -I$(PROJECT_PATH)
CPU-GPU flags with non-managed OpenACC: CXXFLAGS= -fast -acc -ta=tesla,pinned -Minfo=accel -O3 -Wall -std=c++0x -I$(PROJECT_PATH)
Ubuntu - Linux paths: INC_LIB_YAML = ; INC_DIR_YAML = ; INC_LIB_HDF5 = -L/usr/lib/x86_64-linux-gnu/hdf5/openmpi; INC_DIR_HDF5 = -I/usr/include/hdf5/openmpi;
MAC - OS X paths: INC_LIB_YAML = -L/usr/local/lib; INC_DIR_YAML = -I/usr/local/include; INC_LIB_HDF5 = ; INC_DIR_HDF5 = ;

In addition, we have added these examples in the Makefile files of the project. In this regard, the users will only need to comment/uncomment few lines of the Makefile file depending on their computing system.

Best, Lluis

diehlpk commented 1 year ago

@ctdegroot Could you please have a look?

diehlpk commented 1 year ago

@ctdegroot Could you please have a look?

diehlpk commented 1 year ago

@ctdegroot Could you please have a look?

lluisjofre commented 1 year ago

Dear @diehlpk,

Over the past 6 months, we have carefully addressed all the comments raised by the two reviewers about the manuscript (paper.md), README.md file, and software.

In this regard, if possible, we would like to ask if the paper can be accepted in the present format and finalize the review process.

Thanks for your attention and comprehension.

Best, Lluis

ctdegroot commented 1 year ago

My review is complete.

diehlpk commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1016/j.jocs.2017.07.004 is OK
- 10.1115/1.4054554 is OK
- 10.1063/1.3676783 is OK
- 10.1016/j.jcp.2019.01.007 is OK
- 10.1137/S003614450036757X is OK
- 10.1109/MCSE.2013.47 is OK
- 10.1016/j.cpc.2020.107262 is OK
- 10.1016/j.pecs.2020.100877 is OK
- 10.1007/s00158-022-03293-y is OK
- 10.1017/CBO9780511781438 is OK
- 10.1063/1.869966 is OK
- 10.1016/j.cpc.2015.02.008 is OK
- 10.1063/1.4993489 is OK
- 10.1146/annurev.fluid.010908.165248 is OK
- 10.1016/j.jocs.2016.11.001 is OK
- 10.1109/TIM.2022.3165790 is OK
- 10.1016/0021-9991(92)90046-2 is OK
- 10.1146/annurev-fluid-122109-160753 is OK
- 10.1016/j.cpc.2021.107906 is OK
- 10.2514/1.J053813 is OK
- 10.1007/b79761 is OK

MISSING DOIs

- None

INVALID DOIs

- None

diehlpk commented 1 year ago

@editorialbot generate paper

editorialbot commented 1 year ago

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

@editorialbot commands

diehlpk 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:

diehlpk commented 1 year ago

@lluisjofre

[ ] Please generate a new release including all changes during the JOSS review and post the version number here.
[ ] Please upload that version to Zenodo or FigShare and post the DOI here. Note that the title and authors of the paper have to match with the archive.

After that I will recommend your paper for acceptance.

lluisjofre commented 1 year ago

Dear @diehlpk,

We have followed carefully your instructions.

new release generated with version number: v1.0.0
manuscript uploaded to Zenodo with DOI: 10.21105/joss.04637

Best, Lluis

diehlpk commented 1 year ago

@editorialbot set v1.0.0 as version

editorialbot commented 1 year ago

Done! version is now v1.0.0

diehlpk commented 1 year ago

@editorialbot 10.21105/joss.04637 as archive

editorialbot commented 1 year ago

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

@editorialbot commands

diehlpk commented 1 year ago

@editorialbot set 10.21105/joss.04637 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.21105/joss.04637

diehlpk commented 1 year ago

@lluisjofre The DOI does not resolve yet. Can you please post the link to Zenodo?

lluisjofre commented 1 year ago

Dear @diehlpk,

The link to Zenodo is: https://zenodo.org/record/7523172#.Y76HzMHMKUA

Best, Lluis

diehlpk commented 1 year ago

Dear @lluisjofre

I meant to upload the source code of v1.0.0 to Zenodo and not the paper.

Can you please fix that?

Here is some random example from a recent paper: https://zenodo.org/record/7515195

lluisjofre commented 1 year ago

Dear @diehlpk,

We have a question. When you asked to generate a release and upload that version to Zenodo, you were referring to (i) the source code for the JOSS paper or (ii) the source code for the RHEA solver?

Thanks, Lluis

diehlpk commented 1 year ago

For the REHA solver.

lluisjofre commented 1 year ago

Dear @diehlpk,

Ok, thanks. We understand now.

We have generated a new release for the RHEA solver.

the release version is: v1.0.0
the code source has been uploaded to Zenodo with DOI: 10.5281/zenodo.7525886
the weblink to Zenodo is: https://doi.org/10.5281/zenodo.7525886

Best, Lluis

diehlpk commented 1 year ago

@editorialbot add 10.5281zenodo.7525886 as archive

editorialbot commented 1 year ago

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

@editorialbot commands

diehlpk commented 1 year ago

@editorialbot set 10.5281zenodo.7525886 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281zenodo.7525886

diehlpk commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

diehlpk commented 1 year ago

@lluisjofre I recommended your paper for acceptance and it should be published soon.

editorialbot commented 1 year ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3873, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 1 year ago

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

OK DOIs

- 10.1016/j.jocs.2017.07.004 is OK
- 10.1115/1.4054554 is OK
- 10.1063/1.3676783 is OK
- 10.1016/j.jcp.2019.01.007 is OK
- 10.1137/S003614450036757X is OK
- 10.1109/MCSE.2013.47 is OK
- 10.1016/j.cpc.2020.107262 is OK
- 10.1016/j.pecs.2020.100877 is OK
- 10.1007/s00158-022-03293-y is OK
- 10.1017/CBO9780511781438 is OK
- 10.1063/1.869966 is OK
- 10.1016/j.cpc.2015.02.008 is OK
- 10.1063/1.4993489 is OK
- 10.1146/annurev.fluid.010908.165248 is OK
- 10.1016/j.jocs.2016.11.001 is OK
- 10.1109/TIM.2022.3165790 is OK
- 10.1016/0021-9991(92)90046-2 is OK
- 10.1146/annurev-fluid-122109-160753 is OK
- 10.1016/j.cpc.2021.107906 is OK
- 10.2514/1.J053813 is OK
- 10.1007/b79761 is OK

MISSING DOIs

- None

INVALID DOIs

- None

danielskatz commented 1 year ago

@editorialbot set 10.5281/zenodo.7525886 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7525886

danielskatz commented 1 year ago

@lluisjofre - As the track editor who will finish the processing of your submission, I've proofread the paper, and see a number of small issues in the bib file. For some reason, I'm not having success using the GitLab UI, so here is a new bib file that contains the changes. If you can merge this, please do. (note that github won't allow me to post a .bib file here, so I've added .txt to the end, but this file is really paper.bib paper.bib.txt

lluisjofre commented 1 year ago

Dear @danielskatz,

Thanks for proofreading the paper. We have substituted the paper.bib file accordingly.

Best, Lluis

lluisjofre commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

I'm sorry @lluisjofre, I'm afraid I can't do that. That's something only eics are allowed to do.

danielskatz commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1016/j.jocs.2017.07.004 is OK
- 10.1115/1.4054554 is OK
- 10.1063/1.3676783 is OK
- 10.1016/j.jcp.2019.01.007 is OK
- 10.1137/S003614450036757X is OK
- 10.1109/MCSE.2013.47 is OK
- 10.1016/j.cpc.2020.107262 is OK
- 10.1016/j.pecs.2020.100877 is OK
- 10.1007/s00158-022-03293-y is OK
- 10.1017/CBO9780511781438 is OK
- 10.1063/1.869966 is OK
- 10.1016/j.cpc.2015.02.008 is OK
- 10.1063/1.4993489 is OK
- 10.1146/annurev.fluid.010908.165248 is OK
- 10.1016/j.jocs.2016.11.001 is OK
- 10.1109/TIM.2022.3165790 is OK
- 10.1016/0021-9991(92)90046-2 is OK
- 10.1146/annurev-fluid-122109-160753 is OK
- 10.1016/j.cpc.2021.107906 is OK
- 10.2514/1.J053813 is OK
- 10.1007/b79761 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3876, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 year ago

@lluisjofre - I don't see the effect I expected from the bib file changes, and when I look at https://gitlab.com/ProjectRHEA/flowsolverrhea/-/tree/master/paper, I don't see that the file has been updated.

danielskatz commented 1 year ago

ok, now I do - I'll try again

openjournals / joss-reviews