[REVIEW]: SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations #3743

whedon · 2021-09-21T11:31:42Z

Submitting author: @EgorOrachyov (Egor Orachev)
Repository: https://github.com/JetBrains-Research/spbla
Branch with paper.md (empty if default branch): joss-paper
Version: v1.0.0
Editor: @Nikoleta-v3
Reviewers: @mlxd, @bencardoen
Archive: 10.5281/zenodo.7009938

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Review checklist for @abb58

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General checks

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Documentation

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Software paper

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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?

Review checklist for @mlxd

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
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 (@EgorOrachyov) 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 and who the target audience is?
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?

The text was updated successfully, but these errors were encountered:

whedon · 2021-09-21T11:31:46Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @abb58, @mlxd it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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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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whedon · 2021-09-21T11:32:01Z

Wordcount for paper.md is 394

whedon · 2021-09-21T11:32:01Z

PDF failed to compile for issue #3743 with the following error:

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:155:in `block in check_orcids': Problem with ORCID (0000-0000-0000-0000) for Egor Orachev^[co-first author] (RuntimeError)
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:153:in `each'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:153:in `check_orcids'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:90:in `initialize'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:58:in `prepare'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

whedon · 2021-09-21T11:32:02Z

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

OK DOIs

- 10.1186/1471-2105-14-149 is OK
- 10.1145/2499370.2462159 is OK
- 10.1145/3210259.3210264 is OK
- 10.1007/978-3-030-54832-2_6 is OK

MISSING DOIs

- 10.1007/978-3-319-46523-4_38 may be a valid DOI for title: Context-Free Path Queries on RDF Graphs

INVALID DOIs

- None

whedon · 2021-09-21T11:32:12Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.57 s (526.7 files/s, 94282.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                    96           4745           6380          22648
C++                             98           1677           1552           5539
OpenCL                          31            961            215           3345
CUDA                            29            602            605           1850
Python                          20            505            546           1128
Markdown                         8            204              0            708
CMake                            9             85             31            382
Bourne Shell                     6             17             21            109
YAML                             2             14              2            107
TeX                              1              5              0             70
SVG                              2              0              0              2
-------------------------------------------------------------------------------
SUM:                           302           8815           9352          35888
-------------------------------------------------------------------------------


Statistical information for the repository '686d7eec9413c01fa1158df8' was
gathered on 2021/09/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Egor19035                       11          7145            913           11.05
EgorOrachev                      3            11           8250           11.33
Maria Karpenko                  15         45080          11508           77.62

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
EgorOrachev               11123       101118.2          2.7               25.60
Maria Karpenko            33597           74.5          2.5               15.90

Nikoleta-v3 · 2021-09-21T11:33:31Z

@whedon generate pdf from branch joss-paper

whedon · 2021-09-21T11:33:34Z

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon · 2021-09-21T11:34:09Z

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

Nikoleta-v3 · 2021-09-21T11:34:48Z

👋🏼 @EgorOrachyov @abb58, @mlxd this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements 🔝 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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #3743 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 any of you require some more time. We can also use Whedon (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 (@Nikoleta-v3 ) if you have any questions/concerns 👍🏻 😄

Nikoleta-v3 · 2021-09-21T11:37:38Z

@EgorOrachyov please fix the missing DOI: #3743 (comment) :)

EgorOrachyov · 2021-09-21T12:57:57Z

Missing doi fixed! :)

EgorOrachyov · 2021-09-21T12:58:03Z

@whedon generate pdf from branch joss-paper

whedon · 2021-09-21T12:58:06Z

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon · 2021-09-21T12:58:34Z

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

whedon · 2021-10-05T11:31:50Z

👋 @mlxd, please update us on how your review is going (this is an automated reminder).

whedon · 2021-10-05T11:31:50Z

👋 @abb58, please update us on how your review is going (this is an automated reminder).

EgorOrachyov · 2021-10-13T14:28:45Z

@mlxd Hi, thank you for your issue feedback. I hope, we've fixed it! Check out the latest source code version.

mlxd · 2021-10-13T16:43:35Z

@mlxd Hi, thank you for your issue feedback. I hope, we've fixed it! Check out the latest source code version.

Thanks @EgorOrachyov ! I'll try to get around to reviewing these in the coming days.

mlxd · 2021-10-26T09:11:45Z

HI @EgorOrachyov just a quick update. I am having GPU issues at the moment, expect it to be resolved in the coming days and will finish review once done.

Nikoleta-v3 · 2021-11-09T08:09:43Z

Thank you for the update! @abb58, please let us know how your review is going 😄

mlxd · 2021-11-21T11:49:42Z

Apologies for the delays. I have added a new issue for compiling the library at SparseLinearAlgebra/spbla#13

mlxd · 2021-11-21T12:07:30Z

Issue added for adding additional examples: SparseLinearAlgebra/spbla#14

editorialbot · 2022-08-19T11:51:47Z

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

OK DOIs

- 10.1007/978-3-319-46523-4_38 is OK
- 10.1186/1471-2105-14-149 is OK
- 10.1145/2499370.2462159 is OK
- 10.1145/3210259.3210264 is OK
- 10.1007/978-3-030-54832-2_6 is OK
- 10.1145/3322125 is OK
- 10.1016/j.jpdc.2015.06.010 is OK
- 10.1145/2909437.2909442 is OK
- 10.1109/HPEC.2016.7761646 is OK

MISSING DOIs

- 10.1145/3466795 may be a valid DOI for title: GraphBLAST: A High-Performance Linear Algebra-based Graph Framework on the GPU

INVALID DOIs

- None

editorialbot · 2022-08-19T11:53:13Z

👋 @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#3448, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Nikoleta-v3 · 2022-08-19T11:53:20Z

@EgorOrachyov there is a missing DOI. Could you please take care of this? 😄

Nikoleta-v3 · 2022-08-19T11:56:48Z

My apologises for only raising the issue now. I was sure I checked the references 😅

EgorOrachyov · 2022-08-19T12:20:16Z

@Nikoleta-v3 If I understand you correctly, I have to fix doi 10.1145/3466795 for GraphBLATS paper and updated article sources?

EgorOrachyov · 2022-08-19T12:23:41Z

@editorialbot generate pdf

EgorOrachyov · 2022-08-19T12:24:13Z

@Nikoleta-v3 Seems to be fixed now

@EgorOrachyov there is a missing DOI. Could you please take care of this? 😄

editorialbot · 2022-08-19T12:25:07Z

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

Nikoleta-v3 · 2022-08-19T13:22:48Z

@editorialbot check references

editorialbot · 2022-08-19T13:23:42Z

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

OK DOIs

- 10.1007/978-3-319-46523-4_38 is OK
- 10.1186/1471-2105-14-149 is OK
- 10.1145/2499370.2462159 is OK
- 10.1145/3210259.3210264 is OK
- 10.1007/978-3-030-54832-2_6 is OK
- 10.1145/3322125 is OK
- 10.1016/j.jpdc.2015.06.010 is OK
- 10.48550/ARXIV.1908.01407 is OK
- 10.1145/2909437.2909442 is OK
- 10.1109/HPEC.2016.7761646 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Nikoleta-v3 · 2022-08-19T13:29:21Z

dear editors please note that I've set the version to be the tagged release v1.0.0. However,

Release v1.0.0 is ok. (I have made new one especially for Zenodo v1.0.0-zenodo, but it is effectively the same thing)

So the Zenodo archive is based on the tagged release v1.0.0-zenodo. Let me know if I should change the version to be v1.0.0-zenodo instead.

arfon · 2022-08-20T06:57:44Z

@editorialbot recommend-accept

editorialbot · 2022-08-20T06:57:45Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-08-20T06:58:14Z

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

OK DOIs

- 10.1007/978-3-319-46523-4_38 is OK
- 10.1186/1471-2105-14-149 is OK
- 10.1145/2499370.2462159 is OK
- 10.1145/3210259.3210264 is OK
- 10.1007/978-3-030-54832-2_6 is OK
- 10.1145/3322125 is OK
- 10.1016/j.jpdc.2015.06.010 is OK
- 10.48550/ARXIV.1908.01407 is OK
- 10.1145/2909437.2909442 is OK
- 10.1109/HPEC.2016.7761646 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-08-20T06:59:21Z

👋 @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#3449, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon · 2022-08-20T07:01:42Z

@editorialbot accept

editorialbot · 2022-08-20T07:01:43Z

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

editorialbot · 2022-08-20T07:04:30Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-08-20T07:04:31Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.03743 joss-papers#3451
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03743
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2022-08-20T07:24:54Z

@mlxd, @bencardoen – many thanks for your reviews here and to @Nikoleta-v3 for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@EgorOrachyov – your paper is now accepted and published in JOSS ⚡🚀💥

editorialbot · 2022-08-20T07:24:55Z

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

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  <img src="https://joss.theoj.org/papers/10.21105/joss.03743/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03743/status.svg
   :target: https://doi.org/10.21105/joss.03743

This is how it will look in your documentation:

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EgorOrachyov · 2022-08-20T07:43:28Z

Many thanks to joss community for reviewing and editing this submission. We are very pleased that we have an opportunity to finally publish it 🎉🚀

bencardoen · 2022-08-21T17:21:07Z

Congrats on the acceptance @EgorOrachyov
As a general comment, 99% of journals/venues I've interacted with so far could learn a lot of how the review process works here: highly responsive, collaborative, constructive, open, automated where needed, allowing humans to focus on the parts that need human reflection. @arfon @Nikoleta-v3

whedon added CMake Python review Shell labels Sep 21, 2021

whedon assigned Nikoleta-v3 Sep 21, 2021

whedon mentioned this issue Sep 21, 2021

[PRE REVIEW]: SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations #3699

Closed

whedon assigned mlxd Sep 22, 2021

mlxd mentioned this issue Oct 8, 2021

Ensure CUDA architecture is set for targets SparseLinearAlgebra/spbla#9

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Aug 19, 2022

Nikoleta-v3 removed the recommend-accept Papers recommended for acceptance in JOSS. label Aug 19, 2022

Nikoleta-v3 added the recommend-accept Papers recommended for acceptance in JOSS. label Aug 19, 2022

editorialbot added accepted published Papers published in JOSS labels Aug 20, 2022

arfon closed this as completed Aug 20, 2022

editorialbot mentioned this issue Nov 24, 2024

[PRE REVIEW]: gpu-ISTL - Extending OPM Flow with GPU Linear Solvers #7524

Open

[REVIEW]: SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations #3743

[REVIEW]: SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations #3743

Comments

whedon commented Sep 21, 2021 • edited by editorialbot Loading

Status

Reviewer instructions & questions

Review checklist for @abb58

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @mlxd

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Sep 21, 2021

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EgorOrachyov commented Sep 21, 2021

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EgorOrachyov commented Oct 13, 2021

mlxd commented Oct 13, 2021

mlxd commented Oct 26, 2021

Nikoleta-v3 commented Nov 9, 2021

mlxd commented Nov 21, 2021

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Nikoleta-v3 commented Aug 19, 2022

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arfon commented Aug 20, 2022

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