[PRE REVIEW]: GEOS-2024: A portable multi-physics simulation framework

[editorialbot]

Submitting author: !--author-handle-->@rrsettgast<!--end-author-handle-- (Randolph Settgast) Repository: https://github.com/GEOS-DEV/GEOS Branch with paper.md (empty if default branch): docs/JOSS Version: v1.0.1 Editor: !--editor-->@lucydot<!--end-editor-- Reviewers: @MakisH, @timokoch, @berenger-eu Managing EiC: Kristen Thyng

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Markdown: [![status](https://joss.theoj.org/papers/5a00d91636edd7cdf6449776a60dffcf/status.svg)](https://joss.theoj.org/papers/5a00d91636edd7cdf6449776a60dffcf)

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[editorialbot]

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

OK DOIs

- 10.1002/nag.2557 is OK
- 10.1109/P3HPC49587.2019.00012 is OK
- 10.1147/JRD.2019.2954403 is OK
- 10.1007/3-540-47789-6_66 is OK
- 10.1145/1089014.1089021 is OK
- 10.1137/19M1256117 is OK
- 10.1016/j.cma.2021.114111 is OK
- 10.1017/9781009157926 is OK

MISSING DOIs

- No DOI given, and none found for title: CHAI
- No DOI given, and none found for title: PETSc Web page
- No DOI given, and none found for title: GEOS Documentation

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=1.84 s (1344.8 files/s, 352363.0 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C++                             485          24070          16278         115405
SVG                              14             33             70         105329
C/C++ Header                    678          28274          58573          99010
XML                             535           8653           4000          61400
CSV                              47              0              0          60400
reStructuredText                432           9918           7284          14614
Python                          114           3808           2529          13407
CMake                           106           1166            793           4579
XSD                               1              0           1830           3662
YAML                             18            185            271           1684
Bourne Shell                     10            121            112            549
Markdown                         10             80             15            401
Bourne Again Shell               13             99             63            383
Perl                              1             34             76            191
JSON                              5              0              0            116
TeX                               2             15              0            112
diff                              3              9             40             35
INI                               1              9              0             33
make                              1             15              3             21
Dockerfile                        1              1              4             12
CSS                               1              3              3             11
C Shell                           2              3             18              8
--------------------------------------------------------------------------------
SUM:                           2480          76496          91962         481362
--------------------------------------------------------------------------------

Commit count by author:

  1366  Randolph R. Settgast
   315  Christopher Sherman
   276  Benjamin Curtice Corbett
   214  Sergey Klevtsov
   196  Randolph Settgast
   185  Francois Hamon
   131  Nicola Castelletto
   129  Antoine Mazuyer
    99  Arturo Vargas
    89  Matteo Cusini
    77  Thomas Gazzola
    73  TotoGaz
    61  Matthias
    57  Pavel Tomin
    51  Brian Han
    47  Herve Gross
    46  Joshua White
    42  Jian Huang
    38  Sy-Tuan Nguyen
    36  Hui Wu
    33  Andrea Franceschini
    29  Ben Corbett
    27  Thomas GAZZOLA
    25  hannah_mairs
    24  Dickson Kachuma
    24  Xavier Lacoste
    20  tbeltzun
    19  MelReyCG
    19  William R Tobin
    19  Yue Hao
    19  acitrain
    17  Jixiang Huang
    17  Stefano Frambati
    16  Lionel Untereiner
    16  francoishamon
    11  Jacques Franc
    11  Victor A. P. Magri
    10  robinspb
    10  wrtobin
     8  Andrea Borio
     8  shabnamjs
     7  Madonna Yoder
     7  frankfeifan
     7  labesse40
     5  Peter B. Robinson
     5  Randy Settgast
     5  Uncrustify Robot
     5  mndiaye24
     4  Mark Khait
     4  Mohammad Karimi-Fard
     4  Tao Jin
     4  Terry Ligocki
     3  AntoineMazuyer
     3  Ben
     3  Brian Manh Hien Han
     3  Chris White
     3  Ryan Aronson
     3  WuHuiLLNL
     3  andrembcosta
     3  paloma-martinez
     3  sohailwaziri
     2  Arnaud DUDES
     2  Mamadou N'diaye
     2  Matteo
     2  Milad Bader
     2  Tom Byer
     2  Victor A. Paludetto Magri
     2  castelletto1
     2  cmcrook5
     2  jacques
     2  jiemeng-total
     2  mazuyer
     1  AlexandreLapene
     1  Andre Costa
     1  Benjamin Corbett
     1  Bertrand Thierry
     1  Castelletto
     1  Guotong
     1  Hewei Tang
     1  Isaac Ju
     1  Kevin J. Dugan
     1  Pengcheng Fu
     1  Quan Bui
     1  aure-lily
     1  dependabot[bot]
     1  geosadmn
     1  joshwhite
     1  kimtaeho07
     1  matteofrigo5
     1  mkhait
     1  rasimHZ
     1  tony
     1  Łukasz Łaniewski-Wołłk

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1489

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

:warning: An error happened when generating the pdf. Problem with affiliations for Rasim Hasanzade, perhaps the affiliations index need quoting?.

[kthyng]

@rrsettgast can you take a look at the paper error?

[rrsettgast]

Hello @kthyng, Can you help me with some questions I have.

1. Some of the references do not have a DOI. Is this OK?
2. The word count is reported as 1489. This includes every word in the markdown file, but the number of words in the text is closer to 1000. Is this ok?

[rrsettgast]

potential reviewers: Dennis Gläser (dglaeser) Timo Koch (timokoch) Sthavishtha Bhopalam (sthavishtha)

[rrsettgast]

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[rrsettgast]

@editorialbot generate pdf

[editorialbot]

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

[rrsettgast]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

@rrsettgast We encourage authors to keep closer to the 1000 word limit and move content to docs, etc, where possible, but it is a soft limit. Don't worry about it too much.

[kthyng]

Hi @rrsettgast and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

• [x] OSI-approved license
• [x] Installation instructions
• [x] Documentation
• [x] Tests of some sort
• [x] Check paper
• [x] Substantial scholarly effort
• [x] Clear research application/in scope

[kthyng]

Some of the references do not have a DOI. Is this OK?

Yes, if a reference has no possible DOI, that is fine.

[kthyng]

@rrsettgast

• I see in your paper you differentiate from another GEOS. You might want to differentiate with the major python package https://libgeos.org/ too! (it's a pretty major library). Though, it's not necessary if you have a specific reason for listing that other package.
• Your paper needs spaces before some references, for example on lines 57 and 62, please check for others.
• I've run out of time at the moment but it would help if you can point me to the way users can verify that the code is working properly when they're using it (tests or example/demo code).

[rrsettgast]

Hello @kthyng. I have put some responses inline:

• I see in your paper you differentiate from another GEOS. You might want to differentiate with the major python package https://libgeos.org/ too! (it's a pretty major library). Though, it's not necessary if you have a specific reason for listing that other package.

I did this because I am the author of the previous GEOS, and that GEOS had a similar application space. I had to rewrite from scratch when we targeted exascale hardware, and had called the new code GEOSX. Due to some complaints we received that the pronunciation sounded like "GEO-SEX", we decided to take the GEOS name from the abandoned earlier code.

• Your paper needs spaces before some references, for example on lines 57 and 62, please check for others.

got them. I think we are good on this now.

• I've run out of time at the moment but it would help if you can point me to the way users can verify that the code is working properly when they're using it (tests or example/demo code).

There is some information on testing contained in our quick start guide. There is a tutorials section. There is a section on integrated tests. Also there are example sections Basic Examples and Advanced Examples. I didn't really refer to testing in the document as I thought their existence would be implied. Should I add some text in the main document to highlight it?

[rrsettgast]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

Should I add some text in the main document to highlight it?

No that's ok, you just saved me some time in my checks, thanks.

[kthyng]

We have a backlog of submissions so I will add this to our waitlist. Thanks for your patience.

[rrsettgast]

Hi @kthyng. Thanks for help. let me know if there is anything needed to ease the process.

[rrsettgast]

@editorialbot generate pdf

[editorialbot]

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

[rrsettgast]

Hello @kthyng I notice a lot of submissions after this one have moved off the waitlist. Is there something I should do to get help get the ball rolling on this?

[kthyng]

@rrsettgast In my track (Ecology and Earth Sciences) I don't think any more recent than yours have moved off, though I'm not sure — it depends on relevant editor availability. However, there are several that have been waiting quite a bit longer than yours too. We're all doing our best based on the time we can dedicate to JOSS.

[rrsettgast]

Hi @kthyng ok. understood. Thanks!

[lucydot]

Hi @kthyng and @rrsettgast ; I can edit this. I'll assign myself now.

[lucydot]

@editorialbot assign me as editor

[editorialbot]

Assigned! @lucydot is now the editor

[lucydot]

@MakisH @dglaeser @timokoch - hello 👋 . Are you available to review this submission to JOSS?

[MakisH]

@lucydot I can review this submission (FYI: this will be my first review for JOSS). What is the expected timeline?

[rrsettgast]

@lucydot Thanks for picking this up!! Let me know if there is anything I can do make the process easier for you!

[lucydot]

Hi @MakisH - excellent that this will be your first review, always good to bring someone into the fold! I'll be here to answer any questions you have, and the online docs are useful: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

You don't have to do anything right now. I will find another one or two reviewers, and then a new thread will start (which will give clear review instructions). Once that starts we ask that reviews are completed in ~4 weeks. The process is iterative, a conversation back and forth between reviewers/authors/editors, rather than a "one-shot" review, so we ask that the reviews start early in the timeframe. If you have leave planned, let us know, so we have expectations set. I know holidays for many people (myself included) are coming up.

[lucydot]

@editorialbot add @MakisH as reviewer

[editorialbot]

@MakisH added to the reviewers list!

[lucydot]

@dglaeser @timokoch @justinsgray @jamiebramwell - hello 👋 . Are you available to review this submission to JOSS?

[timokoch]

@lucydot I can do a review. However, I'll be away for much of July. It looks like a relatively big complex HPC-focused package. It could be good to have an additional reviewer with good GPU experience.

[lucydot]

Hi @timokoch - great that you can review. And being away in July is fine - it is a time of year when many of us will be taking leave - thanks for the heads up. Also thanks for your suggestion re: GPU expertise 👍

[lucydot]

@editorialbot add @timokoch as reviewer

[editorialbot]

@timokoch added to the reviewers list!

[lucydot]

Reading the GEOS docs it appears that GEOS can run on (and be reviewed using) a number of system types (laptop, HPC, GPU). The pre-requisites for building are here.

@timokoch and @MakisH - a couple of questions to ensure that the reviewer team (I will find one more) can assess the main parallel computing models enabled in GEOS:

• do you have the capability to build/run with MPI?
• do you have the capability to build/run with OpenMP?
• do you have the capability to build/run with GPU-acceleration (via CUDA)?

[lucydot]

Hi @berenger-eu 👋 - are you available to review this submission to JOSS? We have two reviewers who have expertise in multi-physics simulations. Looking for a third with expertise in parallel computing (MPI/OpenMP/GPU), as the software runs using a number of different parallel computing schemes. There is more information in the GEOS docs.

[MakisH]

@timokoch and @MakisH - a couple of questions to ensure that the reviewer team (I will find one more) can assess the main parallel computing models enabled in GEOS:

* do you have the capability to build/run with MPI?

* do you have the capability to build/run with OpenMP?

* do you have the capability to build/run with GPU-acceleration (via CUDA)?

I will run on a laptop with MPI and OpenMP, but not with CUDA.

[berenger-eu]

Yes, I will be able to work on it only end of July, but if that is fine, I agree to review it.

[dglaeser]

@dglaeser @timokoch @JustinSGray @jamiebramwell - hello 👋 . Are you available to review this submission to JOSS?

@lucydot sorry for the late reply! Unfortunately I am too busy at the moment to review this...

[rrsettgast]

Reading the GEOS docs it appears that GEOS can run on (and be reviewed using) a number of system types (laptop, HPC, GPU). The pre-requisites for building are here.

@timokoch and @MakisH - a couple of questions to ensure that the reviewer team (I will find one more) can assess the main parallel computing models enabled in GEOS:

• do you have the capability to build/run with MPI?
• do you have the capability to build/run with OpenMP?
• do you have the capability to build/run with GPU-acceleration (via CUDA)?

Hello all A point of clarification is that GEOS uses a portability layer, and some of the results included in the paper were generated on NVIDIA V100 present on LLNL/Lassen, and the AMD MI250X GPU present on the ORNL/Frontier exascale machine. Regular non-fp64 capable NVIDIA GPU's may be problematic to run GEOS on (for NVIDIA, we haven't tried anything aside from a V100, A100, H100). The AMD GPU's are not readily available outside the US DOE complex, so it may be hard to find someone with access.

Is the review process testing the building, or about running the code examples? There exist publicly accessible docker images which we use as part of our CI process (building and testing) that reviewers can download. These contain the third-party-libraries for GEOS, and as they are the largest challenge to the build process it might be a good place to start. I can provide paths to the docker images from dockerhub if any reviewers would like to go this route.

Thanks!!! Randy S