[REVIEW]: High-performance xPU Stencil Computations in Julia

[whedon]

Submitting author: @omlins (Samuel Omlin)
Repository: https://github.com/omlins/ParallelStencil.jl
Branch with paper.md (empty if default branch): JuliaConProceeding2022
Version: v2
Editor: @fcdimitr
Reviewers: @georgebisbas, @bgeihe
Archive: 10.5281/zenodo.13847580

Status

Status badge code:

HTML: <a href="https://proceedings.juliacon.org/papers/c28f9f11e3123ebaa856aeca43962b5f"><img src="https://proceedings.juliacon.org/papers/c28f9f11e3123ebaa856aeca43962b5f/status.svg"></a>
Markdown: [![status](https://proceedings.juliacon.org/papers/c28f9f11e3123ebaa856aeca43962b5f/status.svg)](https://proceedings.juliacon.org/papers/c28f9f11e3123ebaa856aeca43962b5f)

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

@georgebisbas & @bgeihe, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @fcdimitr 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 ✨

Review checklist for @georgebisbas

Conflict of interest

• As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JuliaCon 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?
• Authorship: Has the submitting author (@omlins) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

Paper format

• Authors: Does the paper.tex file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
• Page limit: Is the page limit for extended abstracts respected by the submitted document?

Content

• Context: is the scientific context motivating the work correctly presented?
• Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
• Results: are the results presented and compared to approaches with similar goals?

Review checklist for @bgeihe

Conflict of interest

• As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JuliaCon 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?
• Authorship: Has the submitting author (@omlins) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

Paper format

• Authors: Does the paper.tex file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
• Page limit: Is the page limit for extended abstracts respected by the submitted document?

Content

• Context: is the scientific context motivating the work correctly presented?
• Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
• Results: are the results presented and compared to approaches with similar goals?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @georgebisbas, @bgeihe 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/JuliaCon/proceedings-review) 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:

1. Set yourself as 'Not watching' https://github.com/JuliaCon/proceedings-review:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (1239.6 files/s, 187708.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           62            887            552           8623
Markdown                         1            130              0            435
YAML                             2              3              2             55
TOML                             6             10              0             54
-------------------------------------------------------------------------------
SUM:                            71           1030            554           9167
-------------------------------------------------------------------------------


Statistical information for the repository '04166151f14578eb224e9fe1' was
gathered on 2023/11/06.
No commited files with the specified extensions were found.

[whedon]

PDF failed to compile for issue #138 with the following error:

 Can't find any papers to compile :-(

[fcdimitr]

@whedon generate pdf from branch JuliaConProceeding2022

[whedon]

Attempting PDF compilation from custom branch JuliaConProceeding2022. Reticulating splines etc...

[whedon]

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

[fcdimitr]

@whedon check references

[fcdimitr]

@whedon check references from branch JuliaConProceeding2022

[whedon]

Attempting to check references... from custom branch JuliaConProceeding2022

[whedon]

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

OK DOIs

- 10.1109/SC41405.2020.00062 is OK
- ??? is OK
- 10.21105/jcon.00068 is OK
- 10.5194/gmd-15-5757-2022 is OK

MISSING DOIs

- 10.1137/141000671 may be a valid DOI for title: Julia: A fresh approach to numerical computing
- 10.1109/tpds.2018.2872064 may be a valid DOI for title: Effective extensible programming: unleashing Julia on GPUs

INVALID DOIs

- None

[fcdimitr]

@whedon remove @sloede as reviewer

[whedon]

OK, @sloede is no longer a reviewer

[fcdimitr]

@whedon add @bgeihe as reviewer

[whedon]

OK, @bgeihe is now a reviewer

[fcdimitr]

@whedon re-invite @bgeihe as reviewer

[whedon]

The reviewer already has a pending invite.

@bgeihe please accept the invite by clicking this link: https://github.com/JuliaCon/proceedings-review/invitations

[fcdimitr]

@bgeihe thank you for volunteering as a reviewer. You can find more details on the JuliaCon review process here. Feel free to ask me any questions you have.

[omlins]

@fcdimitr : here you can find the DOI for the paper: https://doi.org/10.5281/zenodo.13882412
here you can find the DOI for the code: https://doi.org/10.5281/zenodo.13847580
Please excuse the delay.

[luraess]

And as version number we could set and use the v1 tag from the paper.

[luraess]

@fcdimitr could we get the final actions done here in order to have the paper out? Thanks!

[fcdimitr]

@editorialbot set 10.5281/zenodo.13847580 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.13847580

[fcdimitr]

@editorialbot set v1 as version

[editorialbot]

Done! version is now v1

[fcdimitr]

@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

- 10.1137/141000671 is OK
- 10.1109/SC41405.2020.00062 is OK
- 10.48550/arXiv.2211.15716 is OK
- 10.21105/jcon.00068 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.5194/gmd-15-5757-2022 is OK
- 10.1109/P3HPC51967.2020.00006 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Solving Nonlinear Multi-Physics on GPU Supercomput...
- No DOI given, and none found for title: Solving Nonlinear Partial Differential Equations o...
- No DOI given, and none found for title: Development of Multi-GPU Solvers for Nonlinear Mul...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

👋 @JuliaCon/jcon-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 JuliaCon/proceedings-papers#101, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[fcdimitr]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.jcon.00138 proceedings-papers#102
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jcon.00138
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...

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://proceedings.juliacon.org/papers/10.21105/jcon.00138/status.svg)](https://doi.org/10.21105/jcon.00138)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jcon.00138">
  <img src="https://proceedings.juliacon.org/papers/10.21105/jcon.00138/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://proceedings.juliacon.org/papers/10.21105/jcon.00138/status.svg
   :target: https://doi.org/10.21105/jcon.00138

This is how it will look in your documentation:

We need your help!

JuliaCon Proceedings is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://forms.gle/yANMe4c9YmuW9MWcA
• Making a small donation to support our running costs here: https://numfocus.salsalabs.org/donate-to-jcon

[luraess]

Thank you for handling the paper @fcdimitr 🙏 Glad to see it published!

[luraess]

@fcdimitr Can you set the following:

• the code DOI to https://doi.org/10.5281/zenodo.13847579
• the paper DOI to https://doi.org/10.5281/zenodo.13882411
• the paper version to v2

and then trigger the @editorialbot reaccept (maybe running first, if it would work, the recommend-accept command to produce the proof I could check)

[fcdimitr]

@editorialbot set v2 as version

[editorialbot]

Done! version is now v2

[fcdimitr]

@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

- 10.1137/141000671 is OK
- 10.1109/SC41405.2020.00062 is OK
- 10.48550/arXiv.2211.15716 is OK
- 10.21105/jcon.00068 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.5194/gmd-15-5757-2022 is OK
- 10.1109/P3HPC51967.2020.00006 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Solving Nonlinear Multi-Physics on GPU Supercomput...
- No DOI given, and none found for title: Solving Nonlinear Partial Differential Equations o...
- No DOI given, and none found for title: Development of Multi-GPU Solvers for Nonlinear Mul...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing paper acceptance.

[fcdimitr]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 JuliaCon/proceedings-papers#106