[REVIEW]: Spiner: Performance Portable Routines for Generic, Tabulated, Multi-Dimensional Data

[editorialbot]

Submitting author: @Yurlungur (Jonah Miller)
Repository: https://github.com/lanl/spiner
Branch with paper.md (empty if default branch): joss-paper
Version: v1.5.1
Editor: @dfm
Reviewers: @lgarrison, @jzrake
Archive: 10.5281/zenodo.6800124

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/361f13746822fde77cc0f6f0b0b20bbc/status.svg)](https://joss.theoj.org/papers/361f13746822fde77cc0f6f0b0b20bbc)

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

@lgarrison & @jzrake, 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 @dfm 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 @lgarrison

📝 Checklist for @jzrake

[editorialbot]

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (387.9 files/s, 36361.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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Markdown                         2             19              0            161
TeX                              1             15              0            155
YAML                             1              1              4             20
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SUM:                             4             35              4            336
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1217

[editorialbot]

Failed to discover a valid open source license

[editorialbot]

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

[lgarrison]

Review checklist for @lgarrison

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/lanl/spiner?
• 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 (@Yurlungur) 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?

[dfm]

@Yurlungur, @lgarrison, @jzrake — This is the review thread for the paper. All of our communications will happen here from now on. Thanks again for agreeing to participate!

Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. 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 openjournals/joss-reviews#4367 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 the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[dfm]

Failed to discover a valid open source license

Don't worry about this comment from the bot - it expects the code and paper to both be on the same branch, but this is not the case here, and not a problem!

[editorialbot]

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

OK DOIs

- 10.3847/1538-4365/ab007f is OK
- 10.3847/1538-4365/ab09fc is OK
- 10.1088/0264-9381/27/11/114103 is OK
- 10.3847/0004-637X/816/1/44 is OK
- 10.1109/TPDS.2021.3097283 is OK

MISSING DOIs

- Errored finding suggestions for "Sesame: The Los Alamos National Laboratory Equatio...", please try later
- Errored finding suggestions for "Stellar Collapse: Microphysics", please try later
- Errored finding suggestions for "Singularity-EOS: Performance Portable Equations of...", please try later
- Errored finding suggestions for "Singularity-Opac: Performance Portable Opacities", please try later
- Errored finding suggestions for "Phoebus: Phifty One Ergs Blows Up A Star", please try later
- 10.2307/j.ctv6wggx8.17 may be a valid DOI for title: Ports-of-Call
- Errored finding suggestions for "Catch2", please try later
- Errored finding suggestions for "Numerical Recipes with Source Code CD-ROM 3rd Edit...", please try later

INVALID DOIs

- None

[Yurlungur]

Thanks, @lgarrison, @jzrake , @dfm . Looking forward to interacting with you during the review process.

[dfm]

@lgarrison, @jzrake — This is just a little ping to make sure that this review stays on your radar. It's good to start chipping away at the checklists sooner rather than later!

[jzrake]

Review checklist for @jzrake

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/lanl/spiner?
• 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 (@Yurlungur) 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?

[jzrake]

@Yurlungur -- I hope I'm doing this right. Here are two bits of feedback based on my first impression from the PDF writeup.

1. GPU hardware is designed to do interpolation (1d/2d/3d) in hardware as a primitive operation, long before GPGPU was a thing. I think the writeup should state why a software library to do interpolation on the GPU is needed, or is somehow better than what GPUs do in the hardware pipeline.
2. The Statement of Need makes it seem like the primary purpose of the library is for reading opacity tables in hydro codes, which is a relatively specialized application. Is there something about this library which is aimed specifically at such applications, or is the library also intended to offer better (faster?) interpolation for other applications, e.g. image resampling? If it's the specific application, then the Statement of Need should mention (if it's true) that these hydro codes are currently limited either by the accuracy or performance of lookups in the opacity and/or EOS tables.

[Yurlungur]

Thanks, @jzrake It'll take me a little bit to gather a formal response for these comments and implement changes to the manuscript. I should have something soon.

[Yurlungur]

@jzrake thanks for the comments. I just updated the manuscript based on your feedback. The relevant commit is here. Here's a formal little writeup to explain the answers to your questions:

1. It's true that hardware interpolation is required for graphics applications, and is thus a feature for GPUs. Indeed, one of our team members applied texture interpolation as early as 2007. However, we felt a software layer was required for our (and other) scientific applications for several reasons. Texture interpolation, at least on NVIDIA devices, is only single-precision, with interpolation coefficients stored at half-precission. This is often insufficient for scientific applications. Texture interpolation is also rather constrained in application, to only a few stencil patterns and to uniform data only. While Spiner currently limits itself to linear interpolation on uniform data, we wanted to leave the door open to other algorithms. Texture interpolation also does not support multi-dimensional mixed indexing/interpoaltion operations where, say, three indices of a four-dimensional array are interpolated and one is merely indexed into. Texture interpolation also, by design operates performantly on vectors of data only, rather than on a single element. While obviously GPUs are vector machines, downstream applications may want to build more complicated operations on scalar interpoaltion primitives. For example, equation of state lookups often involve a root find on interpolated data, which is easier to reason about in scalar form. Finally, the intent of Spiner is that the same code base can be used both on CPU and GPU, and on whatever comes next. In other words, that the code be portable. This necessitates a software layer of some kind. That said, a specialization of Spiner that uses hardware intrinsics when appropriate would be an interesting topic of future work. We have added comments to the manuscript emphasizing these points.

2. We wrote Spiner out of a specific need for such a capability for equation of state and opacity data for continuum dynamics codes, and thus that has been our focus. To our knowledge there is no such standalone capability in the literature, although individual codes have certainly come up with their own internal solutions. Thus we believe our work fills a gap by being a "plug and play" capability for these codes that does not sacrifice performance. Continuum dynamics codes of this kind are broadly applicable to a large number of precision scientific applications, including but not limited to astrophysics, geophysics, climate modeling, and simulations of interest to national defense. Together these applications use up a very large number of supercomputer cycles available. That said, interpolation is of course a very broad topic and as ou point out Spiner likely has applications beyond hydro codes. However, we haven't thought very deeply about other pplications. We have added a sentence in the statement of need emphasizing that there is no other performance-portable standalone capability that we know of. We also added a comment about other applications.

[jzrake]

@Yurlungur thank you for the thoughtful reply. I hope this content can be included in the PDF writeup, as I think it significantly clarifies the motivation and objectives of the project.

@dfm is the PDF writeup intended to be very concise, or can it be as detailed as the reply above?

EDIT: I only just saw the additions to the PDF writeup. I'll give another round of comments soon, if I have any.

[jzrake]

@editorialbot generate pdf

[editorialbot]

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

[dfm]

@Yurlungur, @jzrake — Re: manuscript scope. Our goal here is for the manuscript to be brief with the documentation page being the primary standalone source of information, so it's generally a good idea to add some words to the documentation whenever you're extending the manuscript. I prefer the manuscript to not have any unique material (everything should be in the docs one way or another), but that's just my preference and not a requirement!

[Yurlungur]

Thanks for the clarification, @dfm. Currently there's no statement of need in the docs. I will add one that mirrors the discussion here and in the manuscript.

Thanks, @jzrake. Please let me know if the additions to the manuscript address concerns, or if I should further extend it based on the discussion here.

[Yurlungur]

☝️ documentation updated in linked PR (now merged).

[lgarrison]

Hi @Yurlungur! I'm working on my review and as per @dfm's suggestion, I'll ask questions as they come up.

On the performance, the results compared to the CPU look impressive, but it still feels like some additional context would be helpful. The paper motivates Spiner by saying the interpolation should not be the limiting factor in a radiation transport simulation—is that now the case? Do you have timings you can share for the interpolation step versus the total time step in a typical simulation?

Alternatively, you could estimate the achieved FLOPs compared to theoretical peak, either by using the CUDA profiler or by estimating the number of operations by hand. Either the % of peak or a comparison to the total simulation time would help contextualize your success here!

Finally, can you clarify in the writeup whether the performance test was done in single or double precision? Perhaps double, since the paper starts by discussing precision limitations in texture interpolation?

[Yurlungur]

Thanks @jzrake @lgarrison ! I appreciate the time you spent engaging with me and the project.

Thanks @dfm I've merged the PR, done a final readthrough, and incremented version number.

• Version number is: v1.5.1
• DOI is: 10.5281/zenodo.6800124

[dfm]

@editorialbot generate pdf

[editorialbot]

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

[dfm]

@editorialbot set 10.5281/zenodo.6800124 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.6800124

[dfm]

@editorialbot set v1.5.1 as version

[editorialbot]

Done! version is now v1.5.1

[dfm]

@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

- 10.3847/1538-4365/ab007f is OK
- 10.3847/1538-4365/ab09fc is OK
- 10.1088/0264-9381/27/11/114103 is OK
- 10.3847/0004-637X/816/1/44 is OK
- 10.1109/TPDS.2021.3097283 is OK

MISSING DOIs

- 10.2307/j.ctv6wggx8.17 may be a valid DOI for title: Ports-of-Call

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#3350, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[dfm]

@Yurlungur — I've now handed this off to the managing editors to do the final processing. There may be some final edits or other changes, but the process should be fairly quick. Thanks again for your submission and for your responses to all the suggestions from @lgarrison and @jzrake!

@lgarrison, @jzrake — Thanks again for your reviews of this submission. Thanks for the time that you took and the thorough and constructive comments that you made. We couldn't do this without you, and I really appreciate you volunteering your time!!

@openjournals/joss-eics — Some notes: (1) @jzrake's checklist does not have the performance box checked because he didn't have the required hardware (see comment: #4367 (comment)), but @lgarrison was able to replicate the results so I'm happy with this as it stands; (2) the bot has gone rogue with it's recommended missing DOI above... I'm not sure what it's thinking!

[danielskatz]

Well, the DOI does lead to a work that matches the title, so I understand why this was offered as a possibility...

Also, I'm the AEiC this week and will check this now

[Yurlungur]

Thanks all!

[danielskatz]

I've suggested some minor changes in 2 PRs, both of which are already merged

[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

- 10.3847/1538-4365/ab007f is OK
- 10.3847/1538-4365/ab09fc is OK
- 10.1088/0264-9381/27/11/114103 is OK
- 10.3847/0004-637X/816/1/44 is OK
- 10.1109/TPDS.2021.3097283 is OK

MISSING DOIs

- 10.2307/j.ctv6wggx8.17 may be a valid DOI for title: Ports-of-Call

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#3351, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

sorry, one more PR: lanl/spiner#44

[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.04367 joss-papers#3352
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04367
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 @Yurlungur (Jonah Miller) and co-authors!!

And thanks to @lgarrison and @jzrake for reviewing, and to @dfm for editing!
We couldn't do this without you

[editorialbot]

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

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