[REVIEW]: Coral: a parallel spectral solver for fluid dynamics and partial differential equations

[whedon]

Submitting author: @BenMql (BENJAMIN MIQUEL)
Repository: https://github.com/BenMql/coral
Version: v1.1.12
Editor: @eloisabentivegna
Reviewer: @robertsawko, @rhaas80
Archive: 10.5281/zenodo.5458888

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Review checklist for @robertsawko

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• 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.

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General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@BenMql) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• 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: Do the authors clearly state 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?

Review checklist for @rhaas80

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@BenMql) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• 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: Do the authors clearly state 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @robertsawko, @rhaas80 it looks like you're currently assigned to review this paper 🎉.

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[whedon]

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

OK DOIs

- 10.1017/jfm.2020.485 is OK

MISSING DOIs

- 10.1103/physrevfluids.4.121501 may be a valid DOI for title: Convection driven by internal heat sources and sinks: Heat transport beyond the mixing-length or “ultimate” scaling regime

INVALID DOIs

- None

[whedon]

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

[whedon]

👋 @robertsawko, please update us on how your review is going.

[whedon]

👋 @rhaas80, please update us on how your review is going.

[eloisabentivegna]

@robertsawko, @rhaas80, could you post a review update?

[rhaas80]

comments working through installation:

• in the git clone command git clone https://github.com/BenMql/coral.git . I would either leave out the dot . or replace by $PWD which is easier to see
• export CORAL_ROOT=$(PWD) is incorrect and must be $PWD or ${PWD} or $(pwd) since there is no PWD executable only, a PWD variable and a pwd executable.
• no link is provided for downloading MKL, would benice to have though Intel seems to restructure their website periodically making this harder
• MKL is not open-source (it is free-as-in-beer but not free-as-in-speech), would be nice to have alternative, also for non-Intel CPUs
• Decomp2d seems to have its own set of dependencies eg FFTE that the Decomp2d_installation file does not mention
• Decomp2d's makefile refers to $(MKL_PATH)/lib/ia32 though by now intel64 ought to be the default choice
• unclear if Decomp2d must be built against FFTW3 (coral is) or if using MKL's FFTW wrapper are ok
  • in the common problems wiki file Word_of_caution_fftw it is stated "In addition, Coral is linked against a patched version of 2decomp. The patch requires that 2decomp uses the fftw3_f03 interface." but nowhere is this shown in the "regular" installation instructions
• FAILURE: at least the clean target assumes that CORAL_ROOT ends in a slash, which is not the case for export CORAL_ROOT=$PWD
• FAILURE: gfortran-10 fails with:

/src/sparse_tools/sparse_manipulations.f90:124:19:

  124 |                    ptr2B, A%ncol, dbeta, ptr2C, A%nrow)
      |                   1
......
  189 |                    ptr2B, A%ncol, dbeta, ptr2C, A%nrow)
      |                   2
Error: Type mismatch between actual argument at (1) and actual argument at (2) (COMPLEX(8)/REAL(8)).

• needs either fix in code or -fallow-argument-mismatch in MPIFLAGS (proper code being preferred)
• OPTIONAL: parallel build using make -j fails since dependencies for module files are not recorded in makefile

[BenMql]

Thank you for your comments.

• ., $PWD and missing slashes issues have been fixed.
• the 2decomp doc now states explicitly that a vanilla fftw is required.
• A link to MKL has been added.
• I share your enthusiasm for "BLAS/LAPACK-vendor" agnostic code. Down the road, my hope is that Coral can be linked to any BLAS/LAPACK library. For the time being though, I stick to MKL as some of their (non standard) routines are used.
• The failures have been addressed in the last commit: the types of two variables are fixed in sparse_manipulation.f90. This is interesting, I never detected them despite an heavy use of pedantic flags and standard-compliance checks (not with gfortran-10 though). (As an aside: Do I understand correctly that the compiler was smart enough to compare lines 124 and 189 and realized that the same routine was suspiciously called twice with different argument types? The error message suggests that the error was not detected by comparing the call to an interface.)
• Happy to read good references about parallel building. Sounds like an interesting feature to include in the future.

[rhaas80]

The argument mismatch is new by gfortran. Apparently such usage was never really allowed by the Fortran standard, but also never really enforced by compilers (though you may want to give eg the Cray compiler a try which in my experience is pickier than gfortran or ifort). You are certainly not the only code tripped up by this, eg https://www.google.com/search?q=gfortran-10+allow-mismatch&ie=utf-8&oe=utf-8 . For gfortran's release announcement about the issue, please see: https://gcc.gnu.org/gcc-10/changes.html#fortran

[BenMql]

Thank you for these details. This feature definitely helped catching a bug which fortunately had no consequences. (Some pointers used to be twice as long as intended, but fortunately their second half was never accessed.)
Anyway, this glitch is fixed now. Let me know if you run into more trouble while compiling.

[BenMql]

@whedon generate pdf

[whedon]

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

[BenMql]

@whedon generate pdf

[whedon]

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

[rhaas80]

In "2_First_run":

• typo" "After edition" should be "After editing"
• should indicate how much memory the sample run takes
• trying the test data on any number of MPI ranks > 1 I get a SEGFAULT with a backtrace and some information that seems to indicate that opt_decomp passed to transpose_y_to_z is incorect. Here's the information:

Thread 1 "coral_LP.exe" received signal SIGSEGV, Segmentation fault.
__memmove_avx_unaligned_erms () at ../sysdeps/x86_64/multiarch/memmove-vec-unaligned-erms.S:262
262     ../sysdeps/x86_64/multiarch/memmove-vec-unaligned-erms.S: No such file or directory.
(gdb) up
#1  0x00007fffecd982fc in ?? () from /usr/lib/x86_64-linux-gnu/libopen-pal.so.40
(gdb) up
#2  0x00007fffecf268aa in ompi_datatype_sndrcv () from /usr/lib/x86_64-linux-gnu/libmpi.so.40
(gdb)
#3  0x00007fffecf732e3 in ompi_coll_base_alltoallv_intra_pairwise ()
   from /usr/lib/x86_64-linux-gnu/libmpi.so.40
(gdb)
#4  0x00007fffe65b0fa2 in ompi_coll_tuned_alltoallv_intra_dec_fixed ()
   from /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_coll_tuned.so
(gdb)
#5  0x00007fffecf2936b in PMPI_Alltoallv () from /usr/lib/x86_64-linux-gnu/libmpi.so.40
(gdb)
#6  0x00007fffed034d0b in pmpi_alltoallv__ () from /usr/lib/x86_64-linux-gnu/libmpi_mpifh.so.40
(gdb)
#7  0x00005555555de192 in decomp_2d::transpose_y_to_z_real (
    src=<error reading variable: value requires 2654208 bytes, which is more than max-value-size>,
    dst=<error reading variable: value requires 2654208 bytes, which is more than max-value-size>,
    opt_decomp=...) at transpose_y_to_z.f90:87
87               real_type, DECOMP_2D_COMM_ROW, ierror)
(gdb) print opt_decomp
$1 = ( xst = (1, 1, 49), xen = (72, 96, 96), xsz = (72, 96, 48), yst = (1, 1, 49), yen = (72, 96, 96), ysz = (72, 96, 48), zst = (1, 49, 1), zen = (72, 96, 96), zsz = (72, 48, 96), x1dist = (72), y1dist = (96), y2dist = (48, 48), z2dist = (48, 48), x1cnts = (331776), y1cnts = (331776), y2cnts = (165888, 165888), z2cnts = (165888, 165888), x1disp = (0), y1disp = (0), y2disp = (0, 165888), z2disp = (0, -322823200), x1count = 331776, y1count = 331776, y2count = 165888, z2count = 165888, even = .TRUE. )

where opt_decomp%z2disp(2) being -322823200 seems like the likely culprit to me.

[rhaas80]

This seems to be due to assuming that allocate would zero initialize the allocated memory. I can make the SEGFAULT go away by adding

    decomp%x1cnts = 0
    decomp%y1cnts = 0
    decomp%y2cnts = 0
    decomp%z2cnts = 0
    decomp%x1disp = 0
    decomp%y1disp = 0
    decomp%y2disp = 0
    decomp%z2disp = 0

just before the prepare_buffer call. It may be good to run the whole code through valgrinds' memcheck tool.

[BenMql]

Roland,

I have fixed the wiki 2_first_run.

I am most grateful for your checks, comments and suggestions.
In 2decomp&fft, the arrays of integers are now initialized to 0 as you suggested (available as the most recent commit to https://github.com/benmql/2decomp_emptyFourierFourier ). This test case has been run through valgrind, with 2 processes. One error was reported after execution, which looks related to library code (and not Coral itself):

==340744== 1 errors in context 1 of 1:
==340744== Syscall param write(buf) points to uninitialised byte(s)
==340744==    at 0x53614BD: ??? (syscall-template.S:84)
==340744==    by 0xF951FC8: ???
==340744==    by 0x4E7DD6B: ??? (in /usr/lib/openmpi/lib/libopen-rte.so.12.0.2)
==340744==    by 0x50F603E: mca_base_framework_close (in /usr/lib/openmpi/lib/libopen-pal.so.13.0.2)
==340744==    by 0x7BAB47C: ???
==340744==    by 0x4E4E439: orte_finalize (in /usr/lib/openmpi/lib/libopen-rte.so.12.0.2)
==340744==    by 0x404F97: ??? (in /usr/bin/orterun)
==340744==    by 0x403615: ??? (in /usr/bin/orterun)
==340744==    by 0x558E83F: (below main) (libc-start.c:291)
==340744==  Address 0xffefff4f4 is on thread 1's stack
==340744==  Uninitialised value was created by a stack allocation
==340744==    at 0xF951F50: ???

No segfault was triggered.

[eloisabentivegna]

Thanks @rhaas80 for your thorough comments, and @BenMql for addressing them promptly!

@robertsawko, do you have any update to report at this stage?

[rhaas80]

Thanks @rhaas80 for your thorough comments, and @BenMql for addressing them promptly!
@eloisabentivegna Sorry about the long delay. I am unfortunately not yet done with the review.

[eloisabentivegna]

@eloisabentivegna Sorry about the long delay. I am unfortunately not yet done with the review.

Thanks for your progress so far, @rhaas80. I can see your checklist is not complete, but your help up to this point is very appreciated.

[whedon]

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

[danielskatz]

@BenMql - I missed one issue, which will be fixed if you merge BenMql/coral#23 (I hope) - Please merge this, and run @whedon generate pdf to check if it looks ok. If so, then please go ahead and

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
• Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

[BenMql]

@whedon generate pdf

[whedon]

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

[danielskatz]

@BenMql - you might want to change the bib entry for your J Fluid Mech paper to have your first initial rather than first name for consistency, but it's not a big deal either way

[BenMql]

@whedon generate pdf

[whedon]

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

[BenMql]

@danielskatz That looks better. The version tag is v1.1.12
What do people customarily do: register the upload on Zenodo as software or publication? (Apologies for the stupid question, but after all there is a paper and a code in the archive.)

[danielskatz]

the repo (which can but doesn't have to include the paper) should be registered as software - some people use https://guides.github.com/activities/citable-code/ and then make a tagged release on github, which creates the zenodo deposit - if you do this, you will then need to change the zenodo metadata to match the paper title and authors manually

[BenMql]

@danielskatz -- the archived Coral v1.1.12 has been uploaded on Zenodo and has received the DOI 10.5281/zenodo.5458888

[danielskatz]

@whedon set v1.1.12 as version

[whedon]

OK. v1.1.12 is the version.

[danielskatz]

@whedon set 10.5281/zenodo.5458888 as archive

[whedon]

OK. 10.5281/zenodo.5458888 is the archive.

[danielskatz]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1017/jfm.2020.485 is OK
- 10.1103/physrevfluids.4.121501 is OK
- 10.1017/S0022112096002789 is OK
- 10.1103/PhysRevFluids.5.113702 is OK
- 10.1103/PhysRevE.70.056312 is OK
- 10.1103/PhysRevResearch.2.023068 is OK
- 10.1016/j.cpc.2019.107110 is OK
- 10.21105/joss.01071 is OK
- 10.1515/jnum-2012-0013 is OK
- 10.5334/jors.237 is OK
- 10.5334/jors.239 is OK

MISSING DOIs

- 10.1063/1.3058072 may be a valid DOI for title: Hydrodynamic and Hydromagnetic Stability

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2569

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2569, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02978 joss-papers#2570
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02978
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

@BenMql - The DOI doesn't yet resolve for me - when it does, I will close this issue and we'll be done.

[BenMql]

Fantastic. Thank you for your assistance.
The DOI doesn't resolve yet for me neither, but it is probably only a question of time.

[danielskatz]

Congratulations to @BenMql (BENJAMIN MIQUEL)!!

(The DOI is now working, so we're done)

And thanks to @eloisabentivegna for editing, and @robertsawko and @rhaas80 for reviewing!
We couldn't do this without you!

[whedon]

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

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