[REVIEW]: Krylov.jl: A Julia basket of hand-picked Krylov methods

[editorialbot]

Submitting author: @amontoison (Alexis Montoison)
Repository: https://github.com/JuliaSmoothOptimizers/Krylov.jl
Branch with paper.md (empty if default branch): joss-paper
Version: v0.9.4
Editor: @jedbrown
Reviewers: @prj-, @LeilaGhaffari
Archive: 10.5281/zenodo.8310030

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/992d8e510f833d2868fce1342dd11d98"><img src="https://joss.theoj.org/papers/992d8e510f833d2868fce1342dd11d98/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/992d8e510f833d2868fce1342dd11d98/status.svg)](https://joss.theoj.org/papers/992d8e510f833d2868fce1342dd11d98)

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

@vchuravy & @prj-, 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 @jedbrown 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 @prj-

📝 Checklist for @LeilaGhaffari

[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=0.18 s (861.9 files/s, 143374.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           94           3395           2620          15713
Markdown                        39            674              0           2421
YAML                            11             25             37            478
TeX                              2              9              0             95
TOML                             3              5              0             53
JSON                             1              0              0             43
Lisp                             1              1              0             20
CSS                              1              4              0             16
Bourne Shell                     1              0              0              6
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                           154           4113           2657          18846
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1723

[editorialbot]

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

OK DOIs

- 10.1145/2049662.2049663 is OK
- 10.1137/141000671 is OK
- 10.5281/zenodo.2655082 is OK
- 10.1080/00029890.1998.12004985 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.1137/1.9780898718003 is OK
- 10.1137/1.9781611970937 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jedbrown]

👋 @prj- and @vchuravy Welcome to JOSS and thanks for agreeing to review! The comments from @editorialbot above outline the review process, which takes place in this thread (possibly with issues filed in the Krylov.jl repository). I'll be watching this thread if you have any questions.

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 this issue 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 a month or two. Please let me know if you require some more time. We can also use editorialbot to set automatic reminders if you know you'll be away for a known period of time.

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

[editorialbot]

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

[vchuravy]

Review checklist for @vchuravy

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/JuliaSmoothOptimizers/Krylov.jl?
• 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 (@amontoison) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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?

[prj-]

Review checklist for @prj-

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/JuliaSmoothOptimizers/Krylov.jl?
• 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 (@amontoison) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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?

[prj-]

Hello @jedbrown and @amontoison, here is the current state of my checklist, with the remaining unticked checkboxes that should be addressed if possible.

Thanks.

General checks

• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

The file LICENSE.md has a leading Copyright (c) 2015-2019: Dominique Orban. It seems outdated, should this be updated? If not, what's copyrighted?

• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.

I don't think the two provided examples enforce a check with respect to a reference solution. The authors do not state as well what should be the solution. This is very minor, but it would be nice to enforce such a check or at least add a comment with the expected solution.

Functionality

• Functionality: Have the functional claims of the software been confirmed?

The second code snippet does not run when CUDA is not available on the system. Could the authors add some minimal error checking (or even better, add a switch to a more conventional CPU backend) to avoid unhandled runtime exceptions?

Software paper

• State of the field: Do the authors describe how this software compares to other commonly-used packages?

Line 22, "Largest collection of Krylov processes and methods", does not seem very relevant to me. First of all, why should quantity matter over quality? Second, though it should certainly be stated that the collection is very complete, it would be more interesting, in my opinion, to justify the use of this package over other Julia alternatives such as KrylovKit, KrylovMethods, IterativeSolvers, and such.

Other minor points

• Line 35, missing if.
• Nvidia should be typeset NVIDIA throughout the document.
• Line 53, missing , before and Intel GPUs.
• Line 72, Operator-vector products and vector operations are the most expensive operations in Krylov.jl. We rely on BLAS routines as much as possible to perform those operations. This statement is not clear to me, isn't the user supposed to provide the operator-vector product, in which case, how can you certify that you are relying on BLAS there as well? I get what you mean, but please rephrase.
• Line 92, the Cholesky factor to model, maybe best rephrased as the Cholesky factor to approximate.

[prj-]

@amontoison, I see all pending MR referencing the present issue have been merged, should I have a fresh look or are you still addressing some other points?

[amontoison]

@prj-, I worked on a last PR yesterday and today to adress all your comments.

The file LICENSE.md has a leading Copyright (c) 2015-2019: Dominique Orban. It seems outdated, should this be updated? If not, what's copyrighted?

Thanks, I updated the LICENSE.md file. (JuliaSmoothOptimizers/Krylov.jl#712)

I don't think the two provided examples enforce a check with respect to a reference solution. The authors do not state as well what should be the solution. This is very minor, but it would be nice to enforce such a check or at least add a comment with the expected solution.

For the reproducibility, I pushed the example files on the branch joss-paper. Each example is in a folder paper/exampleX with Project.toml and Manifest.toml files.
With a julia --project you can start Julia with exactly the same environnement that we used to run the examples.
I also updated the CI script .buildkite/pipeline.yml to run the example files to check that we don't have errors. (see CI builds)
Do you want an additional check to ensure that we have an expected solution?

The second code snippet does not run when CUDA is not available on the system. Could the authors add some minimal error checking (or even better, add a switch to a more conventional CPU backend) to avoid unhandled runtime exceptions?

I added the following test in the second code snippet to ensure that we have the CUDA drivers a NVIDIA GPU available:

if CUDA.functional()
  ...
end

I also updated the documentation (JuliaSmoothOptimizers/Krylov.jl#714) to be sure that users don't try to store and solve linear problems on GPUs if they don't have the hardware associated.

Line 22, "Largest collection of Krylov processes and methods", does not seem very relevant to me. First of all, why should quantity matter over quality? Second, though it should certainly be stated that the collection is very complete, it would be more interesting, in my opinion, to justify the use of this package over other Julia alternatives such as KrylovKit, KrylovMethods, IterativeSolvers, and such.

Krylov.jl represents my thesis work and I see the package as a toolbox of Krylov processes and methods.
As a researcher of new Krylov methods and Krylov processes, I find that it's practical for benchmarking and comparing the behavior of various Krylov subpaces. It's also great for teaching.
The paragraph "Largest collection of Krylov processes and methods" was intended to highlight this characteristic.
I reformulated the parapraph and also mentioned the packages KrylovKit.jl, KrylovMethods.jl and IterativeSolvers.jl.
With the other paragraphs, we try to justify as best we can that we have quantity and quality.

Other minor points

* Line 35, missing `if`.
* `Nvidia` should be typeset `NVIDIA` throughout the document.
* Line 53, missing `,` before `and Intel GPUs`.
* Line 92, `the Cholesky factor to model`, maybe best rephrased as `the Cholesky factor to approximate`.

I fixed these typos in the PR JuliaSmoothOptimizers/Krylov.jl#712.

* Line 72, `Operator-vector products and vector operations are the most expensive operations in Krylov.jl. We rely on BLAS routines as much as possible to perform those operations`. This statement is not clear to me, isn't the user supposed to provide the operator-vector product, in which case, how can you certify that you are relying on BLAS there as well? I get what you mean, but please rephrase.

I clarified and rephrased this sentence in the PR JuliaSmoothOptimizers/Krylov.jl#720.

I will regenerate the PDF of the paper here as soon as the last PR is merged.

[amontoison]

@editorialbot generate pdf

[editorialbot]

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

[prj-]

We are converging... @jedbrown and @amontoison, here is the current state of my checklist, with the remaining unticked checkboxes that should be addressed if possible.

Thanks.

General checks

• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.

You replied: [...] Do you want an additional check to ensure that we have an expected solution?
Yes, it's not because everything is setup to generate a sane environment that the run will necessarily behave correctly, so it would be nice to have a runtime check to ensure that the returned solution is up to a couple of epsilons the same as the expected solution.

Software paper

• State of the field: Do the authors describe how this software compares to other commonly-used packages?

Line 35, Block-Krylov methods should be typeset block Krylov methods. It also appears you do not have implementations of recycling Krylov methods, such as LGMRES, DGMRES, GCRODR, and such, which are available in the literature, but do not feel coerced into adding this in the next revision.

Other minor points

• Line 102, imcomplete
• In the second code snippet, Incomplete Cholesky decomposition should read Incomplete Cholesky factorization for consistency with the rest of the paper

[amontoison]

@editorialbot generate pdf

[editorialbot]

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

[amontoison]

@prj- I updated the paper to address the remaining unticked checkboxes.

[prj-]

Looks good, thanks. There are still a couple of typos, line 97, "In-place methods" (extra s) and line 105, including Sʏᴍᴍʟᴏ̨, Cʀ, and Mɪɴʀᴇs (missing ,), but you can probably wait for the comments of the other reviewer before generating a new proof, it's up to you. I'll have a last look then.

[editorialbot]

Done! version is now v0.9.4

[jedbrown]

@editorialbot set 10.5281/zenodo.8310030 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8310030

[jedbrown]

@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

- 10.1145/2049662.2049663 is OK
- 10.1137/141000671 is OK
- 10.5281/zenodo.2655082 is OK
- 10.1080/00029890.1998.12004985 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.1137/1.9780898718003 is OK
- 10.1137/1.9781611970937 is OK
- 10.2172/1968587 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#4592, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[amontoison]

I found a small bug with the Julia environment, after a ' (adjoint), the color of the code is modified.

[danielskatz]

@amontoison - I'm the track editor who will handle the rest of the process. Later today, I'll proofread this and let you know next steps.

In the meantime, I don't understand the impact of your comment. Are you saying that you need to make a change to the .md file to fix this? If so, please go ahead and then use @editorialbot generate pdf as a new comment to generate a new PDF and check it. If not, please let me know what action you need.

[amontoison]

@danielskatz - Sorry if my comment was not clear. I just remarked that a Julia block of code ('''julia ... ''') is not well displayed.

# Solve Py = x
function ldiv_ic0!(P, x, y, z)
  ldiv!(z, LowerTriangular(P), x)   # Forward substitution with L
  ldiv!(y, LowerTriangular(P)', z)  # Backward substitution with Lᴴ
  return y
end

The issue is related to the lstlisting used by JOSS for the Julia language and not my Markdown file.

[danielskatz]

Do you want us to work on this internally, or should we go ahead and publish, knowing this issue exists?

[danielskatz]

Also, I've proofread the paper, and have a few suggestions, as shown in JuliaSmoothOptimizers/Krylov.jl#809 - please merge this, or let me know what you disagree with.

[amontoison]

Do you want us to work on this internally, or should we go ahead and publish, knowing this issue exists?

I reformulated the second example to avoid this issue (JuliaSmoothOptimizers/Krylov.jl#810).

Also, I've proofread the paper, and have a few suggestions, as shown in JuliaSmoothOptimizers/Krylov.jl#809 - please merge this, or let me know what you disagree with.

I will let @dpo review JuliaSmoothOptimizers/Krylov.jl#809 the final tweaks.

[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

- 10.1145/2049662.2049663 is OK
- 10.1137/141000671 is OK
- 10.5281/zenodo.2655082 is OK
- 10.1080/00029890.1998.12004985 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.1137/1.9780898718003 is OK
- 10.1137/1.9781611970937 is OK
- 10.2172/1968587 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#4621, 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]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Montoison
  given-names: Alexis
  orcid: "https://orcid.org/0000-0002-3403-5450"
- family-names: Orban
  given-names: Dominique
  orcid: "https://orcid.org/0000-0002-8017-7687"
contact:
- family-names: Montoison
  given-names: Alexis
  orcid: "https://orcid.org/0000-0002-3403-5450"
doi: 10.5281/zenodo.8310030
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Montoison
    given-names: Alexis
    orcid: "https://orcid.org/0000-0002-3403-5450"
  - family-names: Orban
    given-names: Dominique
    orcid: "https://orcid.org/0000-0002-8017-7687"
  date-published: 2023-09-26
  doi: 10.21105/joss.05187
  issn: 2475-9066
  issue: 89
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5187
  title: "Krylov.jl: A Julia basket of hand-picked Krylov methods"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05187"
  volume: 8
title: "Krylov.jl: A Julia basket of hand-picked Krylov methods"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot 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.05187 joss-papers#4622
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05187
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 @amontoison (Alexis Montoison) and co-author on your publication!!

And thanks to @prj- and @LeilaGhaffari for reviewing, and to @jedbrown for editing!
JOSS depends on volunteers and we couldn't do this without you

[editorialbot]

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[amontoison]

Thanks @prj-, @LeilaGhaffari, @jedbrown and @danielskatz! 👍 😃 👍