[PRE REVIEW]: GridapSolvers.jl: Scalable multiphysics finite element solvers in Julia #7126

editorialbot · 2024-08-21T12:49:58Z

Submitting author: @JordiManyer (Jordi Manyer)
Repository: https://github.com/gridap/GridapSolvers.jl
Branch with paper.md (empty if default branch): joss-paper
Version: v0.4.0
Editor: @diehlpk
Reviewers: @PetrKryslUCSD, @Leticia-maria
Managing EiC: Daniel S. Katz

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/889d03e60fd6e4c267ca5cbc1cf84e12"><img src="https://joss.theoj.org/papers/889d03e60fd6e4c267ca5cbc1cf84e12/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/889d03e60fd6e4c267ca5cbc1cf84e12/status.svg)](https://joss.theoj.org/papers/889d03e60fd6e4c267ca5cbc1cf84e12)

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editorialbot · 2024-08-21T12:50:02Z

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

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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editorialbot · 2024-08-21T12:50:34Z

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

✅ OK DOIs

- 10.1016/j.cpc.2022.108341 is OK
- 10.1137/141000671 is OK
- 10.21105/JOSS.02520 is OK
- 10.1137/20M1328786 is OK
- 10.1137/100791634 is OK
- 10.1016/j.camwa.2020.06.009 is OK
- 10.1515/jnum-2012-0013 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.1515/jnma-2021-0081 is OK
- 10.1145/1163641.1163644 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1093/acprof:oso/9780199678792.001.0001 is OK
- 10.1137/1.9780898719505 is OK
- 10.1007/978-0-387-09766-4_90 is OK
- 10.21105/joss.04157 is OK
- 10.1145/3445791 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: PETSc/TAO Users Manual
- No DOI given, and none found for title: MPI: A Message-Passing Interface Standard Version ...
- No DOI given, and none found for title: GridapPETSc
- No DOI given, and none found for title: GridapP4est
- No DOI given, and none found for title: PartitionedArrays
- No DOI given, and none found for title: The Trilinos Project Website
- No DOI given, and none found for title: \sl hypre: High Performance Preconditioners
- No DOI given, and none found for title: Preconditing in H(div) and applications
- No DOI given, and none found for title: An implementation of tensor product patch smoother...

❌ MISSING DOIs

- 10.1137/s0895479899358194 may be a valid DOI for title: A Fully Asynchronous Multifrontal Solver Using Dis...
- 10.1145/3242094 may be a valid DOI for title: Performance and Scalability of the Block Low-Rank ...
- 10.1007/pl00005386 may be a valid DOI for title: Multigrid in H (div) and H (curl)

❌ INVALID DOIs

- None

editorialbot · 2024-08-21T12:50:35Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.12 s (1367.5 files/s, 142935.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                          140           2383           1444          10603
TOML                             5            349              2           1496
Markdown                        10            128              0            388
TeX                              1             25              0            308
YAML                             4              1              8            177
Bourne Shell                     6             16             32             76
XML                              1              0              0             20
-------------------------------------------------------------------------------
SUM:                           167           2902           1486          13068
-------------------------------------------------------------------------------

Commit count by author:

   378	JordiManyer
    10	Alberto F. Martin
     2	CompatHelper Julia
     2	amartin
     1	Santiago Badia

editorialbot · 2024-08-21T12:50:41Z

Paper file info:

📄 Wordcount for paper.md is 1728

🔴 Failed to discover a Statement of need section in paper

editorialbot · 2024-08-21T12:50:44Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot · 2024-08-21T12:51:36Z

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

editorialbot · 2024-08-21T12:52:33Z

Five most similar historical JOSS papers:

Gridap: An extensible Finite Element toolbox in Julia
Submitting author: @fverdugo
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @PetrKryslUCSD, @TeroFrondelius, @KristofferC
Similarity score: 0.7520

PyAMG: Algebraic Multigrid Solvers in Python
Submitting author: @lukeolson
Handling editor: @jedbrown (Active)
Reviewers: @mayrmt, @mattmartineau
Similarity score: 0.7389

Krylov.jl: A Julia basket of hand-picked Krylov methods
Submitting author: @amontoison
Handling editor: @jedbrown (Active)
Reviewers: @prj-, @LeilaGhaffari
Similarity score: 0.7265

BasicTools: a numerical simulation toolbox
Submitting author: @fbordeu
Handling editor: @diehlpk (Active)
Reviewers: @hvonwah, @sthavishtha
Similarity score: 0.7248

PDENLPModels.jl: An NLPModel API for Optimization Problems with PDE-Constraints
Submitting author: @tmigot
Handling editor: @jbytecode (Active)
Reviewers: @jmejia8, @HaoZeke
Similarity score: 0.7231

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

danielskatz · 2024-08-21T13:09:10Z

👋 @JordiManyer - thanks for your submission. As the track editor, I'll work on finding an editor. On your side:

Please work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.
Also, please see the example paper about how to cite multiple papers at the same time, and make changes to your .md file.
In your references, please be sure you are not using {{}} around titles that preserve cases, as the JOSS processing determines the cases of words. If you need to preserve a the same in a word or letter, do that with just an extra internal {} where needed. For example, Julia should be {J}ulia in one place I see.
The paper is also a little long - it's about 1800 words, where JOSS papers are typically around 1000 max. Please see if there's anything you can shorten, perhaps by moving it to the repo/documentation and pointing to it there. You can use @editorialbot check repository to see how many words are in the paper.

danielskatz · 2024-08-21T13:10:25Z

👋 @diehlpk - would you be willing to edit this submission?

danielskatz · 2024-08-21T13:10:34Z

@editorialbot invite @diehlpk as editor

editorialbot · 2024-08-21T13:10:37Z

Invitation to edit this submission sent!

JordiManyer · 2024-08-21T13:37:49Z

Hi @danielskatz, thank you for your time. I will look into your comments and let you know if I have any doubts.

JordiManyer · 2024-08-21T13:42:05Z

@danielskatz A first comment: I believe a lot of words are tied to the example. I believe the actual paper is around 1000/1200 words (which is what I thought you guys would be counting). Could I remove the embedded script and point to a file in the repo? I also think it would help readability, but was under the impression that a demo code within the paper was compulsory.

danielskatz · 2024-08-21T13:49:17Z

The review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) do not require or suggest an example in the paper, so moving the example to the repo/docs would be fine.

diehlpk · 2024-08-21T21:51:04Z

@editorialbot add @diehlpk as reviewer

editorialbot · 2024-08-21T21:51:06Z

Can't add reviewers: There is no editor assigned yet

JordiManyer · 2024-08-21T23:13:20Z

@editorialbot check references

editorialbot · 2024-08-21T23:13:41Z

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

✅ OK DOIs

- 10.1016/j.cpc.2022.108341 is OK
- 10.1137/141000671 is OK
- 10.21105/JOSS.02520 is OK
- 10.1137/20M1328786 is OK
- 10.1137/100791634 is OK
- 10.1016/j.camwa.2020.06.009 is OK
- 10.1515/jnum-2012-0013 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.1515/jnma-2021-0081 is OK
- 10.1145/1163641.1163644 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1093/acprof:oso/9780199678792.001.0001 is OK
- 10.1137/1.9780898719505 is OK
- 10.1007/978-0-387-09766-4_90 is OK
- 10.1137/s0895479899358194 is OK
- 10.1145/3242094 is OK
- 10.21105/joss.04157 is OK
- 10.1090/S0025-5718-97-00826-0 is OK
- 10.1007/PL00005386 is OK
- 10.1145/3445791 is OK
- 10.48550/arXiv.2405.19004 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: PETSc/TAO Users Manual
- No DOI given, and none found for title: MPI: A Message-Passing Interface Standard Version ...
- No DOI given, and none found for title: GridapPETSc
- No DOI given, and none found for title: GridapP4est
- No DOI given, and none found for title: PartitionedArrays
- No DOI given, and none found for title: The Trilinos Project Website
- No DOI given, and none found for title: \sl hypre: High Performance Preconditioners

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

JordiManyer · 2024-08-21T23:17:16Z

I think the DOIs missing at this point are just websites and misc references.

JordiManyer · 2024-08-21T23:17:35Z

@editorialbot generate pdf

editorialbot · 2024-08-21T23:18:50Z

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

editorialbot · 2024-08-21T23:19:33Z

Five most similar historical JOSS papers:

Gridap: An extensible Finite Element toolbox in Julia
Submitting author: @fverdugo
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @PetrKryslUCSD, @TeroFrondelius, @KristofferC
Similarity score: 0.7440

PyAMG: Algebraic Multigrid Solvers in Python
Submitting author: @lukeolson
Handling editor: @jedbrown (Active)
Reviewers: @mayrmt, @mattmartineau
Similarity score: 0.7357

Krylov.jl: A Julia basket of hand-picked Krylov methods
Submitting author: @amontoison
Handling editor: @jedbrown (Active)
Reviewers: @prj-, @LeilaGhaffari
Similarity score: 0.7331

PyAMG: Algebraic Multigrid Solvers in Python
Submitting author: @lukeolson
Handling editor: @jedbrown (Active)
Reviewers: @mayrmt, @Jeff-Hadley, @victorapm
Similarity score: 0.7236

BasicTools: a numerical simulation toolbox
Submitting author: @fbordeu
Handling editor: @diehlpk (Active)
Reviewers: @hvonwah, @sthavishtha
Similarity score: 0.7197

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

JordiManyer · 2024-08-21T23:24:44Z

@editorialbot check repository

editorialbot · 2024-08-21T23:25:02Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.12 s (1377.4 files/s, 143900.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                          140           2383           1444          10603
TOML                             5            349              2           1496
TeX                              1             25              0            313
Markdown                        10            111              0            306
YAML                             4              1              8            177
Bourne Shell                     6             16             32             76
-------------------------------------------------------------------------------
SUM:                           166           2885           1486          12971
-------------------------------------------------------------------------------

Commit count by author:

   379	JordiManyer
    10	Alberto F. Martin
     2	CompatHelper Julia
     2	amartin
     1	Santiago Badia

editorialbot · 2024-08-21T23:25:06Z

Paper file info:

📄 Wordcount for paper.md is 1487

🔴 Failed to discover a Statement of need section in paper

editorialbot · 2024-08-21T23:25:08Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

JordiManyer · 2024-08-21T23:34:01Z

@editorialbot generate pdf

editorialbot · 2024-08-21T23:35:17Z

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

editorialbot · 2024-08-21T23:35:59Z

Five most similar historical JOSS papers:

Gridap: An extensible Finite Element toolbox in Julia
Submitting author: @fverdugo
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @PetrKryslUCSD, @TeroFrondelius, @KristofferC
Similarity score: 0.7486

PyAMG: Algebraic Multigrid Solvers in Python
Submitting author: @lukeolson
Handling editor: @jedbrown (Active)
Reviewers: @mayrmt, @mattmartineau
Similarity score: 0.7398

Krylov.jl: A Julia basket of hand-picked Krylov methods
Submitting author: @amontoison
Handling editor: @jedbrown (Active)
Reviewers: @prj-, @LeilaGhaffari
Similarity score: 0.7289

PyAMG: Algebraic Multigrid Solvers in Python
Submitting author: @lukeolson
Handling editor: @jedbrown (Active)
Reviewers: @mayrmt, @Jeff-Hadley, @victorapm
Similarity score: 0.7243

BasicTools: a numerical simulation toolbox
Submitting author: @fbordeu
Handling editor: @diehlpk (Active)
Reviewers: @hvonwah, @sthavishtha
Similarity score: 0.7221

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

JordiManyer · 2024-08-21T23:43:34Z

@danielskatz I've applied a first round of edits. Fixed all the doi-related stuff. We are down to 1500 words, and I don't think there is anything superfluous to remove. I'll be happy to shorten it if the reviewers deem it necessary.

@diehlpk On the topic of reviewers : Since this paper is a natural extension of GridapDistributed.jl, we could probably consider the same list that was considered back then. Namely,

jedbrown
PetrKryslUCSD
Leticia-maria
TeroFrondelius
KristofferC
rouson
tjhei
chrisrichardson
vijaysm
likask

but we would be happy with any other reviewer you consider relevant.

diehlpk · 2024-08-22T03:12:59Z

@editorialbot add @diehlpk as editor

editorialbot · 2024-08-22T03:13:03Z

Assigned! @diehlpk is now the editor

diehlpk · 2024-08-30T09:16:23Z

Hi @PetrKryslUCSD do you have time to review this paper?

diehlpk · 2024-08-30T09:16:56Z

Hi @likask do you have time to review this paper?

diehlpk · 2024-08-30T09:17:21Z

Hi @Leticia-maria do you have time to review this paper?

Leticia-maria · 2024-08-30T10:19:57Z

Hi @Leticia-maria do you have time to review this paper?

Yes! I can review it by the end of next week.

PetrKryslUCSD · 2024-08-30T14:20:14Z

Hi @PetrKryslUCSD do you have time to review this paper?

Yes.

diehlpk · 2024-08-30T15:45:31Z

@editorialbot add @PetrKryslUCSD as reviewer

editorialbot · 2024-08-30T15:45:33Z

@PetrKryslUCSD added to the reviewers list!

diehlpk · 2024-08-30T15:45:56Z

@editorialbot add @Leticia-maria as reviewer

editorialbot · 2024-08-30T15:45:58Z

@Leticia-maria added to the reviewers list!

diehlpk · 2024-08-30T15:47:06Z

@editorialbot start review

editorialbot · 2024-08-30T15:47:10Z

OK, I've started the review over in #7162.

editorialbot added pre-review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Aug 21, 2024

editorialbot added Julia TeX Shell labels Aug 21, 2024

editorialbot assigned diehlpk Aug 22, 2024

editorialbot assigned PetrKryslUCSD Aug 30, 2024

editorialbot assigned Leticia-maria Aug 30, 2024

editorialbot closed this as completed Aug 30, 2024

[PRE REVIEW]: GridapSolvers.jl: Scalable multiphysics finite element solvers in Julia #7126

[PRE REVIEW]: GridapSolvers.jl: Scalable multiphysics finite element solvers in Julia #7126

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edited

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