[REVIEW]: GeophysicalFlows.jl: Solvers for geophysical fluid dynamics problems in periodic domains on CPUs & GPUs #3053

whedon · 2021-02-22T07:57:51Z

Submitting author: @navidcy (Navid C. Constantinou)
Repository: https://github.com/FourierFlows/GeophysicalFlows.jl
Version: v0.12.1
Editor: @pdebuyl
Reviewer: @ranocha, @eviatarbach
Archive: 10.5281/zenodo.4695260

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Repository: Is the source code for this software available at the repository url?
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Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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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: Does the paper have a section titled 'Statement of Need' that clearly states 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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
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?

The text was updated successfully, but these errors were encountered:

whedon · 2021-02-22T07:57:54Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ranocha, @eviatarbach it looks like you're currently assigned to review this paper 🎉.

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whedon · 2021-02-22T07:58:29Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.20 s (232.0 files/s, 43355.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           25           1721            498           4898
Markdown                        13            419              0           1048
YAML                             6             17              8            115
TOML                             3              6              0             53
-------------------------------------------------------------------------------
SUM:                            47           2163            506           6114
-------------------------------------------------------------------------------


Statistical information for the repository 'bb0dae94f28ce15b0204c8e1' was
gathered on 2021/02/22.
No commited files with the specified extensions were found.

whedon · 2021-02-22T07:58:39Z

PDF failed to compile for issue #3053 with the following error:

Can't find any papers to compile :-(

pdebuyl · 2021-02-22T07:59:26Z

@ranocha @eviatarbach make sure to accept the invitation to the reviewers group and to have a look at the reviewer guidelines linked to at the top of this review page.

The review process will happen in this issue page, so questions to the author or to me can be added as comments here.

pdebuyl · 2021-02-22T07:59:30Z

@whedon generate pdf from branch JOSS-paper

whedon · 2021-02-22T07:59:32Z

Attempting PDF compilation from custom branch JOSS-paper. Reticulating splines etc...

whedon · 2021-02-22T08:00:39Z

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

eviatarbach · 2021-02-26T22:59:37Z

Before getting into the rest of the review, I ran into some installation issues on older versions of Julia. On Julia 1.5.3 the installation works fine.

On Julia 1.4.1 (less than a year old), the error FourierFlows/GeophysicalFlows.jl#128 occurs upon first import. I understand this was fixed in GeophysicalFlows.jl version 0.8.1, but that version requires Julia 1.5.0, meaning that the package installation is broken on Julia 1.4.1 (and I assume all versions of Julia between 1.4.0 and 1.5.0). I suggest that either a fix is backported or the package be marked as incompatible with these versions.

I also tried installing it on Julia 1.3.1, which results in an error about unsatisfiable requirements. This one is perhaps not as important because it gives an explicit error at installation time. However, I think it would be good to determine which versions of Julia this package is compatible with at present (especially versions since Julia 1.0.5, the LTS), and state this in the repository README.

navidcy · 2021-02-27T00:10:54Z

Thanks @eviatarbach for pointing this out. I’ll try to sort it out and ping you.

navidcy · 2021-02-27T04:42:59Z

Regarding the error on Julia v1.4, I could fix the issue if I could edit a file from the v0.8.0 release.
how do I do that? or what should I google to figure it out?

pdebuyl · 2021-02-27T07:26:39Z

@navidcy you can issue a bugfix release 0.8.5 if necessary. Google should advise you not to edit the content of the release :-)

Is it necessary to fix older versions for this issue?

navidcy · 2021-03-02T23:02:33Z

hi @eviatarbach, regarding the issue with Julia v1.4.2, I've pushed a bugfix release v0.8.5 which should be fine.

julia> using GeophysicalFlows
[ Info: Precompiling GeophysicalFlows [44ee3b1c-bc02-53fa-8355-8e347616e15e]
[ Info: FourierFlows will use 12 threads
[ Info: FourierFlows will use 12 threads

julia>

and

(@v1.4) pkg> test GeophysicalFlows
    Testing GeophysicalFlows
Status `/private/var/folders/1z/s8gw4q055514jw75ztnclx4h0000gn/T/jl_Mqed4V/Manifest.toml`
  [621f4979] AbstractFFTs v1.0.1
  [79e6a3ab] Adapt v2.4.0
  [56f22d72] Artifacts v1.3.0
  [13072b0f] AxisAlgorithms v1.0.0
  [b99e7846] BinaryProvider v0.5.10
  [fa961155] CEnum v0.4.1
  [052768ef] CUDA v1.3.3
  [d360d2e6] ChainRulesCore v0.9.29
  [944b1d66] CodecZlib v0.7.0
  [34da2185] Compat v3.25.0
  [e66e0078] CompilerSupportLibraries_jll v0.3.4+0
  [a2441757] Coverage v1.2.0
  [c36e975a] CoverageTools v1.2.2
  [864edb3b] DataStructures v0.18.9
  [ffbed154] DocStringExtensions v0.8.3
  [e2ba6199] ExprTools v0.1.3
  [7a1cc6ca] FFTW v1.3.2
  [f5851436] FFTW_jll v3.3.9+7
  [2aec4490] FourierFlows v0.6.8
  [0c68f7d7] GPUArrays v5.2.1
  [61eb1bfa] GPUCompiler v0.6.1
  [44ee3b1c] GeophysicalFlows v0.8.5
  [cd3eb016] HTTP v0.9.5
  [83e8ac13] IniFile v0.5.0
  [1d5cc7b8] IntelOpenMP_jll v2018.0.3+2
  [a98d9a8b] Interpolations v0.13.1
  [033835bb] JLD2 v0.3.3
  [692b3bcd] JLLWrappers v1.2.0
  [682c06a0] JSON v0.21.1
  [929cbde3] LLVM v2.0.0
  [4af54fe1] LazyArtifacts v1.3.0
  [856f044c] MKL_jll v2021.1.1+1
  [1914dd2f] MacroTools v0.5.6
  [739be429] MbedTLS v1.0.3
  [c8ffd9c3] MbedTLS_jll v2.16.8+1
  [872c559c] NNlib v0.7.14
  [ca575930] NetworkOptions v1.2.0
  [6fe1bfb0] OffsetArrays v1.6.1
  [efe28fd5] OpenSpecFun_jll v0.5.3+4
  [bac558e1] OrderedCollections v1.4.0
  [69de0a69] Parsers v1.0.15
  [c84ed2f1] Ratios v0.4.0
  [189a3867] Reexport v0.2.0
  [ae029012] Requires v1.1.2
  [276daf66] SpecialFunctions v1.3.0
  [90137ffa] StaticArrays v0.12.5
  [a759f4b9] TimerOutputs v0.5.8
  [3bb67fe8] TranscodingStreams v0.9.5
  [5c2747f8] URIs v1.2.0
  [efce3f68] WoodburyMatrices v0.5.3
  [83775a58] Zlib_jll v1.2.11+18
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8bb1440f] DelimitedFiles
  [8ba89e20] Distributed
  [b77e0a4c] InteractiveUtils
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [44cfe95a] Pkg
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
[ Info: FourierFlows will use 12 threads
testing on CPU
Test Summary: | Pass  Total
Utils         |    2      2
Test Summary:    | Pass  Total
TwoDNavierStokes |    9      9
Test Summary: | Pass  Total
BarotropicQG  |   18     18
Test Summary:  | Pass  Total
BarotropicQGQL |   14     14
Test Summary: | Pass  Total
SurfaceQG     |    9      9
testing on GPU
Test Summary: | Pass  Total
Utils         |    2      2
┌ Warning: calls to Base intrinsics might be GPU incompatible
│   exception =
│    You called cos(x::T) where T<:Union{Float32, Float64} in Base.Math at special/trig.jl:100, maybe you intended to call cos(x::Float64) in CUDA at /g/data/v45/nc3020/.julia/packages/CUDA/dZvbp/src/device/intrinsics/math.jl:5 instead?
│    Stacktrace:
│     [1] cos at special/trig.jl:100
│     [2] broadcast_kernel at /g/data/v45/nc3020/.julia/packages/GPUArrays/uaFZh/src/host/broadcast.jl:60
└ @ GPUCompiler /g/data/v45/nc3020/.julia/packages/GPUCompiler/GKp4B/src/irgen.jl:68
Test Summary:    | Pass  Total
TwoDNavierStokes |    9      9
Test Summary: | Pass  Total
BarotropicQG  |   18     18
Test Summary:  | Pass  Total
BarotropicQGQL |   14     14
Test Summary: | Pass  Total
SurfaceQG     |    9      9
Test Summary: | Pass  Total
MultilayerQG  |   14     14
Total test time: 1111.3896864
    Testing GeophysicalFlows tests passed

navidcy · 2021-03-02T23:08:49Z

@eviatarbach, regarding supporting Julia's longterm release v1.0.5, we can't be using CUDA.jl (since even v0.1.0 requires Julia v1.3). Unfortunately, the latest GeophysicalFlows.jl version that is supported on Julia v1.0.5 is only v0.5.1.

navidcy · 2021-03-02T23:15:49Z

I have added remark regarding version compatibilities with Julia's releases in the readme; see 1fe5dfc.

pdebuyl · 2021-03-03T14:15:35Z

@navidcy typically a JOSS reviews considers a single version of the software. The version listed upon submission is v0.11.3, may I ask what is the relevance of updating earlier versions?

eviatarbach · 2021-03-03T17:50:13Z

@navidcy Thank you for addressing this issue! It works now on Julia 1.4 for me as well.

@pdebuyl I brought up this issue. I thought that this would be important to address since the installation was failing on even quite recent versions of Julia. I apologize if this was outside the scope of the review.

navidcy · 2021-03-03T20:28:10Z

@pdebuyl, as @eviatarbach explained I was trying to address their remark above. I felt that adding a note in the readme was indeed very appropriate.

pdebuyl · 2021-03-03T20:46:49Z

@eviatarbach this was not out of scope, no problem. I did not get why there was a discussion of older versions of the code but it all makes sense. + There is now a bugfix release and extra information in the README, which is good.

ranocha · 2021-03-04T16:51:40Z

Thanks for creating this nice package (and the basic functionality in FourierFlows.jl), @navidcy et al. Please find below some comments and suggestions.

pdebuyl · 2021-03-04T17:26:53Z

Thank you @ranocha for the review.

The statement of need is supposed to be checked on submission, probably it wasn't because of the non "master" branch for the paper.

navidcy · 2021-03-05T22:23:13Z

@ranocha, I don't really see how I should reformat the file in view of your remark: "You should consider reformatting the license file LICENSE.md such that GitHub recognizes the license type automatically, cf. https://opensource.org/licenses/MIT"

Could you elaborate a bit perhaps?

whedon · 2021-04-19T20:38:11Z

Attempting dry run of processing paper acceptance...

whedon · 2021-04-19T20:38:25Z

PDF failed to compile for issue #3053 with the following error:

 Can't find any papers to compile :-(

pdebuyl · 2021-04-19T20:38:26Z

Thanks @ranocha and @eviatarbach for the review!

pdebuyl · 2021-04-19T20:38:48Z

@whedon accept from branch JOSS-paper

whedon · 2021-04-19T20:38:51Z

Attempting dry run of processing paper acceptance...

whedon · 2021-04-19T20:39:21Z

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

OK DOIs

- 10.1137/141000671 is OK
- 10.21105/joss.02018 is OK
- 10.5194/gmd-9-2793-2016 is OK
- 10.21105/joss.02597 is OK
- 10.5281/zenodo.4686348 is OK
- 10.5670/oceanog.2016.66 is OK
- 10.1103/PhysRevResearch.2.023068 is OK
- 10.5281/zenodo.3551326 is OK
- 10.1017/jfm.2021.247 is OK
- 10.5802/smai-jcm.63 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-04-19T20:39:26Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2247

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2247, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch JOSS-paper

navidcy · 2021-04-19T20:51:39Z

@pdebuyl I just went through the proofs.

Looks good -- I just rephrased a the sentence to reflect that Pearson et al. 2021 is part of what "has been done" and not part of what's "Currently, GeophysicalFlows.jl is used for..." and pushed in JOSS-paper branch. (see FourierFlows/GeophysicalFlows.jl@38af08b).

Can you update the pdf to reflect the latest version?

pdebuyl · 2021-04-19T21:04:21Z

Hi @navidcy I'll let the handling associate editor-in-chief take the update into account. They will take the review process further in this review issue.

arfon · 2021-04-20T08:52:21Z

@whedon accept from branch JOSS-paper

whedon · 2021-04-20T08:52:24Z

Attempting dry run of processing paper acceptance...

whedon · 2021-04-20T08:54:21Z

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

OK DOIs

- 10.1137/141000671 is OK
- 10.21105/joss.02018 is OK
- 10.5194/gmd-9-2793-2016 is OK
- 10.21105/joss.02597 is OK
- 10.5281/zenodo.4686348 is OK
- 10.5670/oceanog.2016.66 is OK
- 10.1103/PhysRevResearch.2.023068 is OK
- 10.5281/zenodo.3551326 is OK
- 10.1017/jfm.2021.247 is OK
- 10.5802/smai-jcm.63 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-04-20T08:56:09Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2248

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2248, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch JOSS-paper

navidcy · 2021-04-20T08:57:48Z

thanks @arfon, looks good!

arfon · 2021-04-21T06:15:01Z

@whedon accept deposit=true from branch JOSS-paper

whedon · 2021-04-21T06:15:04Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2021-04-21T06:16:22Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-04-21T06:16:22Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03053 joss-papers#2253
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03053
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2021-04-21T06:18:50Z

@ranocha, @eviatarbach - many thanks for your reviews here and to @pdebuyl for editing this submission. JOSS relies upon the volunteer efforts of people like you, and we couldn't do this without you ✨

@navidcy - your paper is now accepted into JOSS ⚡🚀💥

whedon · 2021-04-21T06:18:54Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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whedon added Julia review labels Feb 22, 2021

whedon assigned pdebuyl Feb 22, 2021

whedon mentioned this issue Feb 22, 2021

[PRE REVIEW]: GeophysicalFlows.jl: Solvers for geophysical fluid dynamics problems in periodic domains on CPUs & GPUs #2996

Closed

whedon assigned eviatarbach and ranocha Feb 23, 2021

navidcy mentioned this issue Mar 4, 2021

JOSS paper FourierFlows/GeophysicalFlows.jl#187

Closed

This was referenced Mar 4, 2021

Adds Contributor's Guide in Docs + CONTRIBUTING.md FourierFlows/GeophysicalFlows.jl#204

Merged

Examples on GPU FourierFlows/GeophysicalFlows.jl#167

Closed

whedon added accepted published Papers published in JOSS labels Apr 21, 2021

arfon closed this as completed Apr 21, 2021

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[REVIEW]: GeophysicalFlows.jl: Solvers for geophysical fluid dynamics problems in periodic domains on CPUs & GPUs #3053

[REVIEW]: GeophysicalFlows.jl: Solvers for geophysical fluid dynamics problems in periodic domains on CPUs & GPUs #3053

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whedon commented Feb 22, 2021 • edited Loading

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whedon commented Feb 22, 2021

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