[PRE REVIEW]: ADIOS4DOLFINx: A framework for checkpointing in FEniCS

[editorialbot]

Submitting author: @jorgensd (Jørgen Schartum Dokken)
Repository: https://github.com/jorgensd/adios4dolfinx
Branch with paper.md (empty if default branch):
Version: v0.8.0
Editor: @danielskatz
Reviewers: @gonsie, @Chilipp
Managing EiC: Daniel S. Katz

Status

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Thanks for submitting your paper to JOSS @jorgensd. Currently, there isn't a JOSS editor assigned to your paper.

@jorgensd if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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

OK DOIs

- 10.5281/zenodo.10447666 is OK
- 10.1016/j.softx.2020.100561 is OK
- 10.48550/arXiv.2401.05868 is OK
- 10.1145/2998441 is OK
- 10.1145/3524456 is OK

MISSING DOIs

- No DOI given, and none found for title: XDMF and ParaView: checkpointing format
- No DOI given, and none found for title: MPI: A Message-Passing Interface Standard. Version...

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1123.7 files/s, 143945.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          31            947            749           3881
YAML                            12             97             22            379
Markdown                         5             87              0            220
TeX                              1              9              0             69
TOML                             1              9              5             54
reStructuredText                 1              1              2              2
-------------------------------------------------------------------------------
SUM:                            51           1150            778           4605
-------------------------------------------------------------------------------

Commit count by author:

    44	Jørgen S. Dokken
    43	Jørgen Schartum Dokken
    29	Jorgen S. Dokken
    12	Henrik Finsberg
     5	Francesco Ballarin
     3	jorgensd
     1	Joergen Schartum Dokken
     1	Nate

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 942

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[jorgensd]

@editorialbot generate pdf

[danielskatz]

👋 @jorgensd - thanks for your submission. I'll be editing it.

If you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission. You can also suggest people not on the JOSS list.

[danielskatz]

@editorialbot assign me as editor

[editorialbot]

Assigned! @danielskatz is now the editor

[editorialbot]

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

[jorgensd]

👋 @jorgensd - thanks for your submission. I'll be editing it.

If you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission. You can also suggest people not on the JOSS list.

I guess lukeolson might be appropriate.
I've previously worked (and lived with) mscroggs and IgorBaratta, and have co-authored several papers with them, so I guess that excludes them.

[danielskatz]

Yes, folks that you have a conflict of interest with can't review. Note that our COI rule goes back 4 years on previous collaborations, so if something is older than that, it's ok.

A few more suggestions would be welcome.

[danielskatz]

👋 @lukeolson - would you be willing to review this submission for JOSS?

[jorgensd]

Yes, folks that you have a conflict of interest with can't review. Note that our COI rule goes back 4 years on previous collaborations, so if something is older than that, it's ok.

A few more suggestions would be welcome.

What about https://github.com/mikaem? He was a lecturer during my master studies, But that is almost a decade ago.

Or: https://github.com/gonsie or: https://github.com/Chilipp

[danielskatz]

👋 @mikemahoney218, @gonsie, @Chilipp - would one or two of you be willing to review this JOSS submission?

[jorgensd]

👋 @mikemahoney218, @gonsie, @Chilipp - would one or two of you be willing to review this JOSS submission?

Did you mean tagging mikemahoney218 or did you mean mikaem?:)

[danielskatz]

sorry, autocomplete...

[danielskatz]

👋 @mikaem - would you be willing to review this submission for JOSS?

[jorgensd]

@editorialbot generate pdf

[editorialbot]

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

[gonsie]

Count me in!

[Chilipp]

I must admit that I have not yet heard about Dolphin, but I do have some experience in parallelization. If you think that is enough for being a reviewer @jorgensd, I am happy to serve as a reviewer here!

[jorgensd]

I must admit that I have not yet heard about Dolphin, but I do have some experience in parallelization. If you think that is enough for being a reviewer @jorgensd, I am happy to serve as a reviewer here!

The software is a MPI based framework for storing checkpoints (function or mesh data) from simulations from FEniCS, that is a software for solving PDEs with finite elements, and making it compatible across runs with different number of processes.

Most of the actual source code is pure numpy (vectorized) and using MPI neighborhood communicators to transfer these arrays to and from processes, along with using ADIOS2.

I have no issue with you being a reviewer.

[danielskatz]

FYI, the author doesn't actually choose or accept reviewers; this is the role of the editor

But discussion about reviewer suitability is great to have - thanks!

[danielskatz]

@gonsie and @Chilipp - I'm going to go ahead and add both of you and start the review. Thanks very much for agreeing so quickly!

[danielskatz]

@editorialbot add @gonsie as reviewer

[editorialbot]

@gonsie added to the reviewers list!

[danielskatz]

@editorialbot add @Chilipp as reviewer

[editorialbot]

@Chilipp added to the reviewers list!

[danielskatz]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6451.

[jorgensd]

FYI, the author doesn't actually choose or accept reviewers; this is the role of the editor

But discussion about reviewer suitability is great to have - thanks!

I know. Just saying ive got no issues, or conflicts of interest:)