[REVIEW]: PDLSM-FEM: Solver of Coupled Peridynamics Least Squares Minimization with Finite Element Method

[whedon]

Submitting author: @QibangLiu (Qibang Liu)
Repository: https://github.com/QibangLiu/PDLSM-FEM_mpi
Version: v1.0
Editor: @prashjha
Reviewer: @TLCFEM, @karthikncsu, @Balaje
Archive: 10.5281/zenodo.5784823

⚠️ JOSS reduced service mode ⚠️

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Review checklist for @TLCFEM

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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

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• 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: 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?
• 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 @karthikncsu

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@QibangLiu ) 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? #3765
• 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: 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?
• 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 @Balaje

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@QibangLiu ) 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? #3810
• 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: 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?
• 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. @TLCFEM, @karthikncsu, @Balaje it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 556

[whedon]

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

OK DOIs

- doi.org/10.1016/S0022-5096(99)00029-0 is OK
- 10.1007/s10659-007-9125-1 is OK
- 10.1007/s00466-017-1469-1 is OK
- 10.1016/j.cma.2014.06.016 is OK
- 10.1016/j.cma.2019.01.032 is OK
- 10.1016/j.engfracmech.2020.107483 is OK
- 10.1007/s10704-012-9745-8 is OK
- 10.1007/978-1-4614-8465-3 is OK
- 10.1016/j.engfracmech.2021.107862 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.12 s (533.5 files/s, 117414.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             30            930           2024          10106
C/C++ Header                    29            129            166            880
TeX                              1             10              0            110
CMake                            4             13             36             81
Markdown                         2              9              0             32
-------------------------------------------------------------------------------
SUM:                            66           1091           2226          11209
-------------------------------------------------------------------------------


Statistical information for the repository '6da3ee72f6882291fd61d3e9' was
gathered on 2021/08/29.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
QibangLiu                       21         16580           2345          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
QibangLiu                 14235           85.9          2.2               20.79

[whedon]

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

[prashjha]

Thank you, @TLCFEM, @karthikncsu, @Balaje for agreeing to be reviewers. Please read the first couple of comments in this thread and also reviewer guidelines here. Also, you can browse the closed "REVIEW" issues on the "joss-reviews" repository to get some ideas on how to complete the reviews. Thanks again and good luck!

[whedon]

👋 @karthikncsu, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @Balaje, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @TLCFEM, please update us on how your review is going (this is an automated reminder).

[prashjha]

Hello @Balaje @TLCFEM, I am wondering how is the review going?

@karthikncsu please let me know when you can start the review. If you are unable to perform the review, let me know.

[karthikncsu]

@prashjha, Sorry for the delay. I have started the review!

[prashjha]

@karthikncsu great. thanks!! :)

[TLCFEM]

working on it.

[karthikncsu]

@QibangLiu

Installation of the PDLSM-FEM solver software requires setting up the paths for MKLROOT and MPIROOT as mentioned in the manual: page 7 section 2.2 Build on Linux

export MKLROOT =/ homes / MKL_2020 / compilers_and_libraries_2020 .1.217/ linux / mkl
export MPIROOT =/ opt / software / OpenMPI /4.0.5 - iccifort -2020.4.304

I suppose these pathnames are available in the older version of intel parallel studio.

Intel had discontinued the old intel parallel studio product and have released the open-source oneAPI tool kit, replacing Intel Parallel Studio XE on December 8, 2020.

https://software.intel.com/content/www/us/en/develop/tools/oneapi/all-toolkits.html
https://en.wikipedia.org/wiki/Intel_Parallel_Studio

I faced similar issues recently when my intel parallel studio license got expired and had to change my code to be compatible with oneAPI. I am not able to install the package as I don't have the intel parallel studio license. Please modify the code and the documentation with the new paths for the mkl and iccifort filenames in the open API installation directory.

Please let me know if there is an alternate way of installing the software.

[QibangLiu]

@karthikncsu Thanks for your comments. I didn't realize they closed the old version and released the oneAPI toolkit.
The principles to set environment variables are that:
(a) Under the path "MKLROOT/include", there is the "mkl.h file", and under the path "MKLROOT/lib/intel64", there are libraries as the MKL link line advisor show, such as "libmkl_intel_ilp64.so", "libmkl_core.so".
(b) Under the path "MPIROOT/include", there is the header file "mpi.h", and under the path "MPIROOT/lib", there is the library "libmpi.so".
This explanation is added in the manual file.

For the MPIROOT, the OpenMPI is installed under the path "/opt / software / OpenMPI /4.0.5 - iccifort -2020.4.304" on my machine, but not installed with the intel parallel studio product.
Anyway, I modified the values based on the oneAPI toolkit setting as your request:
export MKLROOT=/homes/qibangliu/intel/oneapi/mkl/2021.3.0
export MPIROOT=/homes/qibangliu/intel/oneapi/mpi/2021.3.0

I noted that the file "libmpi.so" is under the path /homes/qibangliu/intel/oneapi/mpi/2021.3.0/lib/release, so the
HINTS value in the FindMPI.cmake file should be modified as:
find_library(MPI_LIBRARY NAMES libmpi.so HINTS $ENV{MPIROOT}/lib $ENV{MPIROOT}/lib/release)

The updates were posted on GitHub.

[QibangLiu]

@whedon generate pdf

[whedon]

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

[QibangLiu]

@whedon check references

[whedon]

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

OK DOIs

- doi.org/10.1016/S0022-5096(99)00029-0 is OK
- 10.1007/s10659-007-9125-1 is OK
- 10.1007/s00466-017-1469-1 is OK
- 10.1016/j.cma.2014.06.016 is OK
- 10.1016/j.cma.2019.01.032 is OK
- 10.1016/j.engfracmech.2020.107483 is OK
- 10.1007/s10704-012-9745-8 is OK
- 10.1007/978-1-4614-8465-3 is OK
- 10.1016/j.engfracmech.2021.107862 is OK
- 10.1007/s42102-021-00060-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[karthikncsu]

Hi @QibangLiu Thank you for updating the manual with the settings to run the PDLSM-FEM with one API.

I tried to install on my ubuntu system and it returned below error:

/opt/intel/oneapi/mkl/2021.3.0//lib/intel64/libmkl_gnu_thread.so: undefined reference to GOMP_loop_end_nowait' /opt/intel/oneapi/mkl/2021.3.0//lib/intel64/libmkl_gnu_thread.so: undefined reference to GOMP_loop_ordered_static_start'
/opt/intel/oneapi/mkl/2021.3.0//lib/intel64/libmkl_gnu_thread.so: undefined reference to omp_get_thread_num' /opt/intel/oneapi/mkl/2021.3.0//lib/intel64/libmkl_gnu_thread.so: undefined reference to GOMP_loop_dynamic_next'
/opt/intel/oneapi/mkl/2021.3.0//lib/intel64/libmkl_gnu_thread.so: undefined reference to GOMP_sections_next' /opt/intel/oneapi/mkl/2021.3.0//lib/intel64/libmkl_gnu_thread.so: undefined reference to GOMP_parallel_end'
/opt/intel/oneapi/mkl/2021.3.0//lib/intel64/libmkl_gnu_thread.so: undefined reference to omp_get_num_threads' /opt/intel/oneapi/mkl/2021.3.0//lib/intel64/libmkl_gnu_thread.so: undefined reference to omp_set_max_active_levels'
/opt/intel/oneapi/mkl/2021.3.0//lib/intel64/libmkl_gnu_thread.so: undefined reference to `GOMP_parallel_sections_start'
collect2: error: ld returned 1 exit status
CMakeFiles/PDLSM-FEM.dir/build.make:854: recipe for target 'PDLSM-FEM' failed
make[2]: *** [PDLSM-FEM] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/PDLSM-FEM.dir/all' failed
make[1]: *** [CMakeFiles/PDLSM-FEM.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2

Let me know a way around to resolve this. I would also recommend you to provide requirements files in the Github repo.

[TLCFEM]

need flag -fopenmp

[prashjha]

@whedon check references

[whedon]

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

OK DOIs

- doi.org/10.1016/S0022-5096(99)00029-0 is OK
- 10.1007/s10659-007-9125-1 is OK
- 10.1007/s00466-017-1469-1 is OK
- 10.1016/j.cma.2014.06.016 is OK
- 10.1016/j.cma.2019.01.032 is OK
- 10.1016/j.engfracmech.2020.107483 is OK
- 10.1007/s10704-012-9745-8 is OK
- 10.1007/978-1-4614-8465-3 is OK
- 10.1016/j.engfracmech.2021.107862 is OK
- 10.1007/s42102-021-00060-3 is OK
- 10.1016/j.engfracmech.2009.02.016 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[prashjha]

Hi @QibangLiu, could you address these points:

1. Draft corrections (suggestions):

• Line 7: I will suggest removing single quote around PDLSM-FEM solver
• Line 8: "and 3D using MPI parallelism" instead of "3D by MPI technique"?
• Line 8, 9: "This cross-platform solver is written in a C++ language and includes ..."?
• Line 27: "that of a PD with a spherical neighborhood"?
• Line 27: "However, their PD ..."?
• Line 37: you have used "much" multiple times and further "much" sounds not so scientific. How about "... mesh relatively fast and utilizes less memory compared to pure PD model implementations."?
• Line 39: In "In many published PD...", please specify references as "many" does not sound right.
• Line 44: "... in an easy way similar to FEM without introducing fictitious layer"?
• Line 44: "... solver enables two criteria ..."?
• Line 45: In "for 2D crack ...", is it just for 2D or is it is true also for 3D?
• Line 49: "It can also be ..."?

2. Once you have updated the draft, can you also do a 'tagged' release of your code, and

3. archive the release using zenedo or other methods.

Once you are done, I will run a few commands and hand your paper to EiC for the final decision.

[QibangLiu]

@whedon generate pdf

[whedon]

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

[QibangLiu]

Hello, @prashjha Thanks for your comments and your effort on the paper. I have updated the draft, tagged the code, and archived the release on zenedo. The DOI is
10.5281/zenodo.5784823

Also, Thanks very much for the review, @Balaje @karthikncsu @TLCFEM

[prashjha]

@whedon set 10.5281/zenodo.5784823 as archive

[whedon]

OK. 10.5281/zenodo.5784823 is the archive.

[prashjha]

Thanks, @QibangLiu. One last thing: could you change the title in zenodo archive to match the title of joss paper?

[QibangLiu]

@prashjha DONE.

[prashjha]

Great...handing it to EiC!!

[prashjha]

@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

- doi.org/10.1016/S0022-5096(99)00029-0 is OK
- 10.1007/s10659-007-9125-1 is OK
- 10.1007/s00466-017-1469-1 is OK
- 10.1016/j.cma.2014.06.016 is OK
- 10.1016/j.cma.2019.01.032 is OK
- 10.1016/j.engfracmech.2020.107483 is OK
- 10.1007/s10704-012-9745-8 is OK
- 10.1007/978-1-4614-8465-3 is OK
- 10.1016/j.engfracmech.2021.107862 is OK
- 10.1007/s42102-021-00060-3 is OK
- 10.1016/j.engfracmech.2009.02.016 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2830

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2830, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kyleniemeyer]

@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.03668 joss-papers#2833
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03668
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...

[kyleniemeyer]

Congratulations @QibangLiu on your article's publication in JOSS!

Many thanks to @TLCFEM, @karthikncsu, and @Balaje for reviewing this submission, and @prashjha for editing.

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03668/status.svg)](https://doi.org/10.21105/joss.03668)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03668">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03668/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03668/status.svg
   :target: https://doi.org/10.21105/joss.03668

This is how it will look in your documentation:

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