[REVIEW]: Accelerating Parallel Operation for Compacting Selected Elements on GPUs

[editorialbot]

Submitting author: @yogi-tud (Johannes Fett)
Repository: https://github.com/yogi-tud/space_gpu
Branch with paper.md (empty if default branch):
Version: 1.0
Editor: @danielskatz
Reviewers: @robertszafa, @wimvanderbauwhede
Archive: 10.5281/zenodo.6884000

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/46f248b28d020ee9c15a463a130544bb"><img src="https://joss.theoj.org/papers/46f248b28d020ee9c15a463a130544bb/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/46f248b28d020ee9c15a463a130544bb/status.svg)](https://joss.theoj.org/papers/46f248b28d020ee9c15a463a130544bb)

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

@robertszafa & @wimvanderbauwhede, 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 @danielskatz 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 @robertszafa

📝 Checklist for @wimvanderbauwhede

[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:

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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]

Software report:

github.com/AlDanial/cloc v 1.88  T=1.32 s (1072.1 files/s, 242003.0 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
CUDA                            502          24816          32955          94842
C/C++ Header                    641          15793          43769          62412
C++                             161           4935           3557          19975
Markdown                         12           1107              0           3938
CMake                            60            711           1208           3478
Python                           11            926           1132           2220
make                             12            146            141            471
Perl                              1             99             41            461
Bourne Again Shell                6            119            151            430
SVG                               1              0              1            271
YAML                              6             21             20            198
Bourne Shell                      6             32              8            130
TeX                               1              3              0             25
--------------------------------------------------------------------------------
SUM:                           1420          48708          82983         188851
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 430

[editorialbot]

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

OK DOIs

- 10.15803/ijnc.7.2_208 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[danielskatz]

👋 @robertszafa and @wimvanderbauwhede - Thanks for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#4589 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

[robertszafa]

Review checklist for @robertszafa

Conflict of interest

• 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

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

General checks

• Repository: Is the source code for this software available at the https://github.com/yogi-tud/space_gpu?
• 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 (@yogi-tud) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• 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?

[robertszafa]

Hi @yogi-tud, I've added a few issues related to documentation. The rest looks good to me.

[yogi-tud]

Hi @robertszafa
Thanks for the input. I have added the documentation and a readme file providing an example.
Also some information about contributing in a file called CONTRIBUTE.

[wimvanderbauwhede]

Review checklist for @wimvanderbauwhede

Conflict of interest

• 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

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

General checks

• Repository: Is the source code for this software available at the https://github.com/yogi-tud/space_gpu?
• 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 (@yogi-tud) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• 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?

[wimvanderbauwhede]

@editorialbot commands

[editorialbot]

Hello @wimvanderbauwhede, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[wimvanderbauwhede]

@danielskatz All issues are closed, both forms completed @robertszafa

[danielskatz]

@editorialbot generate pdf

[editorialbot]

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

[danielskatz]

@yogi-tud - I'm suggesting a number of small changes to your paper in yogi-tud/space_gpu#4. In addition, I think a reference would be useful for "the NVIDIA-supplied CUB library" Once this is done, we can move to the final acceptance steps

[yogi-tud]

@danielskatz There is already a reference to the cub main page. I renamed it to "NVIDIA CUB library" in the bib.
Is that okay?

[yogi-tud]

@editorialbot generate pdf

[editorialbot]

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

[danielskatz]

ok, thanks.

[danielskatz]

@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

- 10.15803/ijnc.7.2_208 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-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/joss-papers#3391, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04589 joss-papers#3392
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04589
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @yogi-tud (Johannes Fett) and co-authors!

And thanks to @robertszafa and @wimvanderbauwhede for reviewing!
We couldn't do this without you

[danielskatz]

I'm going to leave this open for now, as I realize we had intended to mention Euro-Par in the final published PDF, which I think @arfon will need to do manually.

[yogi-tud]

Thanks for the review and the smooth editorial process.

[danielskatz]

Also @wimvanderbauwhede, do we know the DOI for the Euro-Par paper? If so, we could also mention that in the left column, as we do with AAS-partnered papers, such as in https://joss.theoj.org/papers/10.21105/joss.04417

[wimvanderbauwhede]

@danielskatz I have the DOIs for the conference papers but they are not live yet so if we put them in the JOSS paper they won't work yet.

[danielskatz]

@wimvanderbauwhede - Can we continue this discussion in the email I sent you around the same time as the comment above?

[arfon]

@yogi-tud – could you please merge this PR to associate this submission with your Europar submission? yogi-tud/space_gpu#5

[arfon]

@editorialbot generate pdf

[yogi-tud]

@arfon I just merged your MR.

[editorialbot]

⚠️ An error happened when generating the pdf.

[arfon]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#3411

[arfon]

What do you think @wimvanderbauwhede and @danielskatz?: https://github.com/openjournals/joss-papers/blob/e881a2735349adace33e66f83a60aab1852227a7/joss.04589/10.21105.joss.04589.pdf

[danielskatz]

looks good to me - https://joss.theoj.org/papers/10.21105/joss.04589

[wimvanderbauwhede]

Yes, looks good, thanks!

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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