[REVIEW]: ASGarD: Adaptive Sparse Grid Discretization

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@quantumsteve@jedbrown<!--end-editor-- Reviewers: @joglekara, @gnorman7 Archive: Pending

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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

@joglekara & @gnorman7, 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:

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✨ 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 @gnorman7

editorialbot commented 1 month ago

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editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.29 s (591.7 files/s, 221011.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             68           4362           2094          27754
C/C++ Header                    75           3457           4071          18683
CMake                            8            162            249           1112
Markdown                         7             84              0            288
MATLAB                           4             58             21            211
YAML                             3              6             12            182
Bourne Shell                     1              4             38            113
TeX                              1              7              0             88
Python                           1             15              1             27
CSS                              1              4              3             20
-------------------------------------------------------------------------------
SUM:                           169           8159           6489          48478
-------------------------------------------------------------------------------

Commit count by author:

   497  Benjamin T. McDaniel
   439  Tyler McDaniel
   170  Graham Lopez
   169  Steven Hahn
   114  Cole Kendrick
    93  David Green
    46  Miroslav Stoyanov
    30  Coleman Kendrick
    30  elwasif
    20  none
    19  adam-mcdaniel
    16  Harry Hughes
    11  Stefan Schnake
     7  Hugo Brunie
     7  Mark Cianciosa
     7  Tim Younkin
     7  Timothy Younkin
     7  Tyler
     6  Eirik Endeve
     5  McDaniel, Benjamin T
     4  stefan-schnake
     3  David L Green
     3  Green, David L
     3  T McDaniel
     1  Brian Friesen
     1  Justin Burzachiello
     1  Lopez
     1  hl8

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1034

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

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

OK DOIs

- 10.1016/j.jcp.2017.10.009 is OK
- 10.1063/1.4776712 is OK
- 10.1063/1.3167820 is OK

MISSING DOIs

- No DOI given, and none found for title: High-dimensional partial differential equations in...
- 10.1088/1361-6544/ac337f may be a valid DOI for title: Algorithms for Solving High Dimensional PDEs: From...
- No DOI given, and none found for title: Sparse-grid Discontinuous Galerkin Methods for the...

INVALID DOIs

- https://doi.org/10.1016/j.jco.2010.04.001 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cpc.2020.107412 is INVALID because of 'https://doi.org/' prefix

editorialbot commented 1 month ago

License info:

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

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

jedbrown commented 1 month ago

Hi, @joglekara, @gnorman7 👋 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 ASGarD 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, the 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.

gnorman7 commented 1 month ago

Review checklist for @gnorman7

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/project-asgard/asgard?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@quantumsteve) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

gnorman7 commented 1 month ago

I was able to set up and run everything without any hiccups, although I did not verify the claims of the MATLAB share engine or plotting. The examples nicely showcase both basic examples and more complicated core functionality (adaptivity). I did not look at any cases beyond slight changes to the examples.

My only negative notes are about referring to other packages.

I'm unsure of the state of the field, or if there are other packages that do Sparse Grid with DG (even non-adaptive). That being said, there are few mentions to other commonly-used packages (although the authors mention other techniques, such as Monte Carlo and the "combination technique"). I do think there could be more referring to similar packages, even if they are not in the same niche.

I think it might be worth mentioning the "separate MATLAB implementation https://github.com/project-asgard/DG-SparseGrid" more prominently. This package seems quite closely related.

quantumsteve commented 3 weeks ago

@gnorman7 Thank you for taking the time to review ASGarD. We are glad to hear you successfully set up and ran everything without hiccups.

In response to your notes, we added a state of the field section to the paper and reference both GalerkinSparseGrids.jl and AdaM-DG. Both combine the discontinuous Galerkin method and sparse grids and AdaM-DG supports adaptivity and shared-memory parallelism. They currently are missing ASGarD's support for GPU accelerators and distributed memory parallelism.

quantumsteve commented 3 weeks ago

The MATLAB code DG-Sparse-Grid hasn't been updated in several years and is no longer maintained or kept up to date with ASGarD. I added a note with this information at the top of the README.

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