[REVIEW]: MoFEM: An open source, parallel finite element library

[whedon]

Submitting author: @likask (Lukasz Kaczmarczyk)
Repository: https://bitbucket.org/likask/mofem-cephas
Version: v0.9.0-joss
Editor: @jedbrown
Reviewers: @tjhei, @chrisrichardson, @Kevin-Mattheus-Moerman, @vijaysm, @chennachaos
Archive: 10.5281/zenodo.3627253

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/43d9625e5ed28d5c493bfc0fae6d8215"><img src="http://joss.theoj.org/papers/43d9625e5ed28d5c493bfc0fae6d8215/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/43d9625e5ed28d5c493bfc0fae6d8215/status.svg)](http://joss.theoj.org/papers/43d9625e5ed28d5c493bfc0fae6d8215)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@tjhei & @chrisrichardson, @Kevin-Mattheus-Moerman, @vijaysm, & @chennachaos, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jedbrown know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @tjhei

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: v0.9.0-joss
• Authorship: Has the submitting author (@likask) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @chrisrichardson

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: v0.9.0-joss
• Authorship: Has the submitting author (@likask) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @Kevin-Mattheus-Moerman

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: v0.9.0-joss
• Authorship: Has the submitting author (@likask) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @vijaysm

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: v0.9.0-joss
• Authorship: Has the submitting author (@likask) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @chennachaos

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: v0.9.0-joss
• Authorship: Has the submitting author (@likask) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tjhei, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

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:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[jedbrown]

@tjhei @chrisrichardson @Kevin-Mattheus-Moerman 👋 Welcome and thanks for agreeing to review! The comments from @whedon above outline the review process, which takes place in this thread (possibly with issues filed in the MoFem repository). I'll be watching this thread if you have any questions.

[likask]

Thank you all for agreeing to spend some time on this. Making life easier, to kick start installation, you can use docker & spack as follows:

git clone --recurse-submodules https://bitbucket.org/likask/mofem-cephas.git mofem-cephas
cd mofem-cephas
docker build -t spack_mofem_build --force-rm=true --file=Dockerfile-spack-mofem-testing .

[chrisrichardson]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

[chrisrichardson]

@likask - https://bitbucket.org/likask/mofem-cephas/src/joss/media/paper.md seems not to work. Is this the correct URL anyway?

[likask]

@chrisrichardson Hello, I had to move paper to the directory visible by whedon to generate PDF. You will find it here https://bitbucket.org/likask/mofem-cephas/src/master/joss/paper.md

See here to view compiled PDF

[chrisrichardson]

@likask - it seems like something must be wrong though. The URL is supposed to point at the software, not the paper?

Repository: Is the source code for this software available at the repository url?

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[arfon]

@likask - it seems like something must be wrong though. The URL is supposed to point at the software, not the paper?

I've updated the URL for the software at the top of the review issue.

[whedon]

👉 Check article proof 📄 👈

[likask]

@arfon Thank you.

@chrisrichardson Source for a master branch is here. Alternatively, you can browse in doxygen generated web-pages here.

[vijaysm]

@likask Please update the version number being reviewed to v0.8.23 if necessary.

Also, fix the broken link to the paper as well. I see your comment above but it would be good to have this propagated on this issue page if possible.

[likask]

I think that version could be bumped at the very end. If you are looking for the source of the paper, it is here link. That is in joss folder in root repo directory in the master branch.

[likask]

@jedbrown are you aware of any major problem enabling to reviewers kick start or complete review? Can I be any help?

[jedbrown]

@likask I'm not aware of any issues. Two reviewers have started ticking boxes in the review. I'll start reminding in a couple weeks if there is no further visible progress.

[Kevin-Mattheus-Moerman]

@jedbrown I'll provide my review by the end of this week. Apologies for the delay so far.

[Kevin-Mattheus-Moerman]

@likask can you point me to some more basic documentation on how to get started to run some examples. I did the following as you suggested:

git clone --recurse-submodules https://bitbucket.org/likask/mofem-cephas.git mofem-cephas
cd mofem-cephas
docker build -t spack_mofem_build --force-rm=true --file=Dockerfile-spack-mofem-testing .

I then studied this demo, went to: /mofem-cephas/mofem/users_modules/basic_finite_elements/nonlinear_elasticity/examples/dam and ran:

mpirun -np 4 ../../nonlinear_dynamics \
-my_file dam.h5m \
-ksp_type fgmres \
-pc_type lu -pc_factor_mat_solver_package mumps \
-ksp_atol 1e-10 -ksp_rtol 1e-12 -ksp_monitor \
-snes_type newtonls -snes_linesearch_type basic \
-snes_max_it 10 -snes_atol 1e-4 -snes_rtol 1e-8 -snes_monitor \
-ts_monitor -ts_type alpha -ts_dt 0.002 \
-ts_final_time 8 -ts_max_snes_failures -1 \
-my_time_data_file dam_history.in \
-my_accelerogram accelerogram.in \
-my_solve_at_time_zero 1 \
-my_output_prt -1 -my_max_post_proc_ref_level 0 \
-my_disp_order 2 \
-default_material HOOKE -is_linear -snes_lag_jacobian -2 \
-elastic_material_configuration block_data.in 2>&1 | tee log

This resulted in:

mpirun was unable to launch the specified application as it could not access
or execute an executable:

Executable: ../../nonlinear_dynamics
Node: newton

while attempting to start process rank 0.

[likask]

@Kevin-Mattheus-Moerman I apologise for the confusion, I put this to run units tests in the docker. We are using that for testing. I see that you run this successfully for core lib and users modules,

core
users modules

If you like to run some particular cases, is better to use spack on the system. However, if you like you, you can execute the dam example as follows

Run docker container

docker run --rm=true -it -v pwd/mofem:/mofem -v $HOME:$HOME -e HOSTHOME=$HOME spack_mofem_build /bin/bash

In doceker

cd /mofem_build/um/build/basic_finite_elements/nonlinear_elasticity
make
cp /mofem/users_modules/basic_finite_elements/nonlinear_elasticity/examples/dam/* .
/mofem_build/um/um_view/bin/mpirun --allow-run-as-root -np 4 ./nonlinear_dynamics \
-my_file dam.h5m  \
-ksp_type fgmres -pc_type lu -pc_factor_mat_solver_package mumps -ksp_atol 1e-10 -ksp_rtol 1e-12 -ksp_monitor \
-snes_type newtonls -snes_linesearch_type basic -snes_max_it 10 -snes_atol 1e-4 -snes_rtol 1e-8 -snes_monitor \
-ts_monitor -ts_type alpha -ts_dt 0.002 -ts_final_time 8 -ts_max_snes_failures -1 \
-my_time_data_file dam_history.in -my_accelerogram accelerogram.in -my_solve_at_time_zero 1 \
-my_output_prt -1 -my_max_post_proc_ref_level 0 \
-my_disp_order 2 -default_material HOOKE -is_linear -snes_lag_jacobian -2 \
-elastic_material_configuration block_data.in 2>&1 | grep -v "Read -1" | tee log

[Kevin-Mattheus-Moerman]

@likask I'm not a C++ specialist and this is also my first real experience with Docker. Part of the dam example ran using the above code (which is not trivial to set up, should you simplify this and create a run_dam_example script?). Also the dam models takes very long to run. How can a user see how long the model has to go? Can you add a progress indicator e.g. steps 50 of 100 or 50%.

Can you create (or point me to) an extremely simple, e.g. uniaxial tension of a cube, example that runs really fast?

Can you add documentation on how to visualize the results? How can I do do_vtk.sh out_values_*h5m from Docker? How do I use ParaView from Docker? Or how do I get at the files generated in Docker from outside the Docker session?

[whedon]

OK. v0.9.0-joss is the version.

[jedbrown]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.2172/970174 is OK
- 10.1002/nme.847 is OK
- 10.1137/11082539x is OK
- 10.1016/j.camwa.2015.04.027 is OK
- 10.1016/j.cma.2017.06.001 is OK
- 10.1016/j.compositesb.2019.03.027 is OK
- 10.1007/BF00298636 is OK
- 10.5281/zenodo.789521 is OK
- 10.1093/imanum/drq047 is OK
- 10.1515/jnma-2019-0064 is OK
- 10.11578/dc.20171025.1248 is OK
- 10.11578/dc.20171025.1248 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.11588/ans.2015.100.20553 is OK
- 10.1515/jnum-2012-0013 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#1247

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1247, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[jedbrown]

@openjournals/joss-eics 👋 We're ready for you.

[likask]

Thank you all @jedbrown @tjhei @vijaysm @chennachaos @Kevin-Mattheus-Moerman @chrisrichardson

Time, help and patience. Experience with the open journal and open review is great.

[labarba]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.2172/970174 is OK
- 10.1002/nme.847 is OK
- 10.1137/11082539x is OK
- 10.1016/j.camwa.2015.04.027 is OK
- 10.1016/j.cma.2017.06.001 is OK
- 10.1016/j.compositesb.2019.03.027 is OK
- 10.1007/BF00298636 is OK
- 10.5281/zenodo.789521 is OK
- 10.1093/imanum/drq047 is OK
- 10.1515/jnma-2019-0064 is OK
- 10.11578/dc.20171025.1248 is OK
- 10.11578/dc.20171025.1248 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.11588/ans.2015.100.20553 is OK
- 10.1515/jnum-2012-0013 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#1248

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1248, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[labarba]

@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.01441 joss-papers#1249
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01441
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...

[labarba]

Congratulations, @likask, your JOSS paper is published! 🚀

Huge thanks to our editor, @jedbrown, and to the hard-working team of reviewers here! JOSS depends on volunteers like you, and we are grateful 🙏

[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.01441/status.svg)](https://doi.org/10.21105/joss.01441)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01441">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01441/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01441/status.svg
   :target: https://doi.org/10.21105/joss.01441

This is how it will look in your documentation:

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Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
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[likask]

@labarba @jedbrown It is possible to fix link to the repository? See the following
https://bitbucket.org/likask/mofem-cephas/src/joss/media/paper.md

An error was created on very beginning by me from misunderstanding how Weldon searching for the location of paper.md. The fix is simple, the link has to be changed to https://bitbucket.org/likask/mofem-cephas

[labarba]

Yikes.

@openjournals/dev The author notifies us of a mistake in the repository URL, post-publication. Can you help?

[arfon]

@openjournals/dev The author notifies us of a mistake in the repository URL, post-publication. Can you help?

Fixed!