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

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@yogi-tud@danielskatz<!--end-editor-- Reviewers: @robertszafa, @wimvanderbauwhede Archive: 10.5281/zenodo.6884000

Status

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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 commented 2 years ago

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

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editorialbot commented 2 years ago

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 commented 2 years ago

Wordcount for paper.md is 430

editorialbot commented 2 years ago

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 commented 2 years ago

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

danielskatz commented 2 years ago

👋 @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 commented 2 years ago

Review checklist for @robertszafa

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://github.com/yogi-tud/space_gpu?
[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 (@yogi-tud) 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 2 years ago

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

yogi-tud commented 2 years ago

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 commented 2 years ago

Review checklist for @wimvanderbauwhede

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://github.com/yogi-tud/space_gpu?
[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 (@yogi-tud) 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

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 commented 2 years ago

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

danielskatz commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

danielskatz commented 2 years ago

@yogi-tud - I'm suggesting a number of small changes to your paper in https://github.com/yogi-tud/space_gpu/pull/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 commented 2 years ago

@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 commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

danielskatz commented 2 years ago

ok, thanks.

danielskatz commented 2 years ago

At this point could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

yogi-tud commented 2 years ago

I have a question about meta data in Zenodo. Should it be "publication" or "software"?

danielskatz commented 2 years ago

Software. The archival deposit is mainly of the software, though the source of the publication may also in the archived repo

yogi-tud commented 2 years ago

https://doi.org/10.5281/zenodo.6884000

I uploaded the 1.0 release which was just created from the github repo to zenodo. As my funding institutions were not listes as possible options, I did not add them unter the optional funding category.

danielskatz commented 2 years ago

@editorialbot set 10.5281/zenodo.6884000 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6884000

danielskatz commented 2 years ago

@editorialbot set 1.0 as version

editorialbot commented 2 years ago

Done! version is now 1.0

danielskatz commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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 commented 2 years ago

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

danielskatz commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

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

Here's what you must now do:

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

Any issues? Notify your editorial technical team...

danielskatz commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

Thanks for the review and the smooth editorial process.

danielskatz commented 2 years ago

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 commented 2 years ago

@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 commented 2 years ago

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

arfon commented 2 years ago

@yogi-tud – could you please merge this PR to associate this submission with your Europar submission? https://github.com/yogi-tud/space_gpu/pull/5

arfon commented 2 years ago

@editorialbot generate pdf

yogi-tud commented 2 years ago

@arfon I just merged your MR.

editorialbot commented 2 years ago

:warning: An error happened when generating the pdf.

arfon commented 2 years ago

@editorialbot reaccept

editorialbot commented 2 years ago

Rebuilding paper!

editorialbot commented 2 years ago

🌈 Paper updated!

New PDF and metadata files :point_right: https://github.com/openjournals/joss-papers/pull/3411

arfon commented 2 years ago

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

openjournals / joss-reviews