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mfem

License Repo check Build Analysis Builds and Tests Build Status Doxygen

How to Contribute

The MFEM team welcomes contributions at all levels: bugfixes; code improvements; simplifications; new mesh, discretization or solver capabilities; improved documentation; new examples and miniapps; HPC performance improvements; etc.

MFEM is distributed under the terms of the BSD-3 license. All new contributions must be made under this license.

If you plan on contributing to MFEM, consider reviewing the issue tracker first to check if a thread already exists for your desired feature or the bug you ran into. Use a pull request (PR) toward the mfem:master branch to propose your contribution. If you are planning significant code changes or have questions, you may want to open an issue before issuing a PR. In addition to technical contributions, we are also interested in your results and simulation images, which you can share via a pull request in the mfem/web repo.

See the Quick Summary section for the main highlights of our GitHub workflow. For more details, consult the following sections and refer back to them before issuing pull requests:

Contributing to MFEM requires knowledge of Git and, likely, finite elements. If you are new to Git, see the GitHub learning resources. To learn more about the finite element method, see our FEM page.

By submitting a pull request, you are affirming the Developer's Certificate of Origin at the end of this file.

Quick Summary

  • We encourage you to join the MFEM organization and create development branches off mfem:master.
  • Please follow the developer guidelines, in particular with regards to documentation and code styling.
  • Please do not commit large/binary files to the central repository (use a fork instead).
  • Pull requests should be issued toward mfem:master. Make sure to check the items off the Pull Request Checklist and follow the MFEM PR Rules.
  • When your contribution is fully working and ready to be reviewed, add the ready-for-review label.
  • PRs are treated similarly to journal submission with an "editor" assigning two reviewers to evaluate the changes.
  • The reviewers have 3 weeks to evaluate the PR and work with the author to fix issues and implement improvements.
  • During review there should be no force pushes/rewriting history in the branch.
  • After approval, MFEM developers merge the PR manually in the mfem:next branch.
  • After a week of testing in mfem:next, the original PR is merged in mfem:master.
  • We use milestones to coordinate the work on different PRs toward a release.
  • Don't hesitate to contact us if you have any questions.

Code Overview

Source code structure:

The MFEM library uses object-oriented design principles which reflect, in code, the independent mathematical concepts of meshing, linear algebra and finite element spaces and operators.

The MFEM source code has the following structure:

  .
  ├── config
  │   ├── cmake
  │   └── githooks
  ├── data
  ├── doc
  ├── examples
  │   ├── amgx
  │   ├── caliper
  │   ├── ginkgo
  │   ├── hiop
  │   ├── jupyter
  │   ├── petsc
  │   ├── pumi
  │   ├── sundials
  |   └── superlu
  ├── fem
  │   ├── ceed
  │   ├── fe
  │   ├── qinterp
  │   └── tmop
  ├── general
  ├── linalg
  │   └── simd
  ├── mesh
  ├── miniapps
  │   ├── adjoint
  │   ├── autodiff
  │   ├── common
  │   ├── electromagnetics
  │   ├── gslib
  │   ├── meshing
  │   ├── mtop
  │   ├── navier
  │   ├── nurbs
  │   ├── parelag
  │   ├── performance
  │   ├── shifted
  │   ├── solvers
  │   ├── tools
  │   └── toys
  └── tests
      ├── convergence
      ├── gitlab
      ├── mem_manager
      ├── par-mesh-format
      ├── scripts
      └── unit

Main directories and classes

The main directories are fem/, mesh/ and linalg/ containing the C++ classes implementing the finite element, mesh and linear algebra concepts respectively.

Parallel implementation

Parallel MPI objects in MFEM inherit their serial counterparts, so a parallel mesh for example is just a serial mesh on each task plus the information on shared geometric entities between different tasks. The parallel source files have a p prefix, e.g. pmesh.cpp vs. the serial mesh.cpp.

GPU and general device support

GPU and multi-core CPU support is based on device kernels supporting different backends (CUDA, OCCA, RAJA, OpenMP, etc.) and an internal lightweight device/host memory manager.

Utilities, building and documentation

  • The general/ directory contains C++ classes that serve as utilities for communication, error handling, arrays, (Boolean) tables, timing, etc.
  • The config/ directory contains build-related files, both for the plain Makefile and the CMake build options.
  • The doc/ directory contains configuration for the Doxygen code documentation that can either be built locally or browsed online at https://mfem.github.io/doxygen/html/index.html.

Examples and tests

  • examples and miniapps respectively gather simple and more fully-featured demonstrations of the usage on MFEM. They both rely on data/ for the collection of meshes.
  • The tests/ directory contains a unit test suite and will later contain more tests that run example codes.

See also the code overview section on the MFEM website.

GitHub Workflow

The MFEM GitHub organization: https://github.com/mfem, is the main developer hub for the MFEM project.

If you plan to make contributions or would like to stay up-to-date with changes in the code, we strongly encourage you to join the MFEM organization.

This will simplify the workflow (by providing you additional permissions), and will allow us to reach you directly with project announcements.

MFEM Organization

Getting started (GitHub)

Before you can start, you need a GitHub account, here are a few suggestions:

Joining

Structure

  • The MFEM source code is in the mfem repository.
  • The website and corresponding documentation are in the web repository.
  • The PyMFEM repository contains a Python wrapper for MFEM.
  • The data repository contains additional (large) datafiles for MFEM.

New Feature Development

  • A new feature should be important enough that at least one person, the author, is willing to work on it and be its champion.

  • The author creates a branch for the new feature (with suffix -dev), off the master branch, or another existing feature branch, for example:

    # Clone assuming you have setup your ssh keys on GitHub:
git clone [email protected]:mfem/mfem.git

# Alternatively, clone using the "https" protocol:
git clone https://github.com/mfem/mfem.git

# Create a new feature branch starting from "master":
git checkout master
git pull
git checkout -b feature-dev

# Work on "feature-dev", add local commits
# ...

# (One time only) push the branch to github and setup your local
# branch to track the github branch (for "git pull"):
git push -u origin feature-dev

  • We prefer that you create the new feature branch inside the MFEM organization as opposed to in a fork. This allows everyone in the community to collaborate in one central place.

    • If you prefer to work in your fork, please enable upstream edits.

    • Never use the next branch to start a new feature branch!

  • The typical feature branch name is new-feature-dev, e.g. pumi-dev. While not frequent in MFEM, other suffixes are possible, e.g. -fix, -doc, etc.

Developer Guidelines

  • Keep the code lean and as simple as possible

    • Well-designed simple code is frequently more general and powerful.
    • Lean code base is easier to understand by new collaborators.
    • New features should be added only if they are necessary or generally useful.
    • Introduction of language constructions not currently used in MFEM should be justified and generally avoided (to maintain portability to various systems and compilers, including early access hardware).
    • We prefer basic C++ and the C++03 standard, to keep the code readable by a large audience and to make sure it compiles anywhere.

  • Keep the code general and reasonably efficient

    • The main goal is fast prototyping for research and application development.
    • When in doubt, generality wins over efficiency.
    • Respect the needs of different users (current and/or future).

  • Keep things separate and logically organized

    • General usage features go in MFEM (implemented in as much generality as possible), non-general features go into external apps.
    • Inside MFEM, compartmentalize between linalg, fem, mesh, GLVis, etc.
    • Contributions that are project-specific or have external dependencies are allowed (if they are of broader interest), but should be #ifdef-ed and not change the code by default.

  • Code specifics

    • All new public, protected, and private classes, methods, data members, and functions have Doxygen-style documentation in source comments.
    • In addition to arguments and functionality, documentation should include the current limitations of the code, any background information that is implicitly assumed in the implementation, and the ownership and lifetime of data.
    • Consistent code styling is enforced with make style in the top-level directory. This requires Artistic Style (we specifically use version 3.1). See also the file config/mfem.astylerc.
    • Use mfem::out and mfem::err instead of std::cout and std::cerr in internal library code. (You can use std in examples and miniapps.)
    • When manually resolving conflicts during a merge, make sure to mention the conflicted files in the commit message.
    • All significant new features and changes should be documented in CHANGELOG.
    • New examples and miniapps should have documentation on the MFEM webpage.

Pull Requests

  • When your branch is ready for other developers to review / comment on the code, create a pull request towards mfem:master.

  • Pull request typically have titles like:

    Description [new-feature-dev]

    for example:

    Parallel Unstructured Mesh Infrastructure (PUMI) integration [pumi-dev]

    Note the branch name suffix (in square brackets).

  • Titles may contain a prefix in square brackets to emphasize the type of PR. Common choices are: [DON'T MERGE], [WIP] and [DISCUSS], for example:

    [DISCUSS] Hybridized DG [hdg-dev]

  • If the PR is still a work in progress, add the WIP label to it and optionally the [WIP] prefix in the title.

  • Add a description, appropriate labels and assign yourself to the PR. The MFEM team will add reviewers as appropriate.

  • List outstanding TODO items in the description, see PR #222 for an example.

  • When your contribution is fully working and ready to be reviewed, add the ready-for-review label.

  • PRs are treated similarly to journal submission with an "editor" assigning two reviewers to evaluate the changes. The reviewers have 3 weeks to evaluate the PR and work with the author to implement improvements and fix issues.

  • Once the ready-for-review label has been applied and reviewers have been assigned, the PR is considered under review. To help with the review process there should be no force pushes/rewriting history in the branch.

  • After approval, the PR is tested for a week with other approved PRs in the mfem:next branch.

  • Consider manually running the tests in tests/scripts before merging in mfem:next, see the README file in that directory for more details.

  • Track the GitHub Actions and Appveyor continuous integration builds at the end of the PR. These should generally run clean, so address any errors as soon as possible. Please ask if you are unsure how to do that.

  • Note that some tests, such as the branch-history check in GitHub Actions are safeguards that are allowed to fail in certain cases.

  • Other tests, such as the code-style, documentation and gitignore checks in GitHub Actions enforce MFEM-specific rules which are explained in the error messages and the tests/scripts directory.

  • Also note that the tests branch-history and repos-checks found in GitHub Actions can be triggered automatically before each push using git hooks. See the git hooks README for a detailed explanation.

  • If triggered, track the status of the LLNL GitLab tests. If failing, ask one of the LLNL developers for details.

MFEM PR Rules

The Pull Request (PR) approval process in MFEM is similar to the approval of papers in a peer-reviewed journal. In particular:

  1. There is an MFEM board of "editors" that evaluates new PRs and assigns "reviewers" for each PR.

  2. The assigned reviewers are responsible to carefully review and test the proposed PR.

  3. A PR can be (manually) merged in the next branch only if 2 of the assigned reviewers have approved it and it has passed internal testing. This merge can be performed by any of the assigned reviewers or by any of the editors.

  4. A PR can be merged in the master branch only if it has been tested successfully for a week in next and an editor has (optionally) taken a final look. This merge can be performed only by one of the editors.

Responsibilities of Editors

The current list of MFEM editors is:

  • @v-dobrev (Veselin Dobrev)
  • @tzanio (Tzanio Kolev)
  • @pazner (Will Pazner)
  • @mlstowell (Mark Stowell)

The responsibilities of the editors are:

  1. To assign appropriate milestone and labels for new PRs, e.g. bugfix, minor, api-change, high-impact, etc.

  2. To assign at least 2 reviewers for new PRs. An editor can also be a reviewer. The editor, reviewers, and author should be listed as "Assignees" on the GitHub PR page. After assignment, the in-review label should be added.

  3. To complete the initial PR evaluation and assignments in a timely manner: 1 week from submission.

  4. To assist reviewers when they need help with their reviews (but also to stay out of the way when they don't).

  5. To remind the reviewers about timely completion of their review.

  6. To take a final look and complete the PR merge in master. The final look step is optional and shouldn't take more than 3 days.

  7. The assignment of bugfixes should be expedited proportional to their importance, e.g. in some cases the editor can assign much shorter review window.

Responsibilities of Reviewers

Everyone on the MFEM team can be asked to serve as a reviewer on a PR in their area of expertise.

The responsibilities of the reviewers are:

  1. To let the editors know if the proposed assignment is not a good match for them.

  2. To communicate with the PR author, provide feedback and work with them to resolve issues.

  3. To ensure the quality of the PR by making sure that the code adheres to the Developer Guidelines, e.g. all methods, data members, and functions have documentation, including data ownership and lifetime, new examples/miniapps have a corresponding PR in mfem/web, major features have CHANGELOG entries, etc.

  4. To seek help from the editors in case of difficulties.

  5. To complete the review in a timely manner: 3 weeks from assignment.

  6. To test the PR thoroughly before merging in next. The PR author is also encouraged to perform testing and inform the reviewers about the results.

  7. To monitor the PR impact on the testing in the next branch and alert the editors that the PR is ready for merging in master.

  8. The review of bugfixes should be expedited proportional to their importance. The review window can be much less than three weeks in such cases.

Responsibilities of Authors

Authors should clearly indicate when a PR is ready for review (before that the PR should be marked as Draft or [WIP]).

The responsibilities of the authors are:

  1. To follow the instructions and PR checklist in the CONTRIBUTING.md document in the MFEM repository.

  2. To respond to reviewer feedback in a timely manner.

  3. Authors are encouraged to perform testing and inform the reviewers about the results.

  4. Authors can use the "Reviewers" section of the GitHub PR page to suggest reviewers, but the "Assignees" section will show who the editor has assigned to do the reviews.

  5. To indicate when the PR is ready for review by adding the ready-for-review label.

Pull Request Checklist

Before a PR can be merged, it should satisfy the following:

  • Code builds.
  • Code passes make style.
  • Update CHANGELOG:
    • Is this a new feature users need to be aware of? New or updated example or miniapp?
    • Does it make sense to create a new section in the CHANGELOG to group with other related features?
  • Update INSTALL:
    • Had a new optional library been added? If so, what range of versions of this library are required? (Make sure the external library is compatible with our BSD license, e.g. it is not licensed under GPL!)
    • Have the version ranges for any required or optional libraries changed?
    • Does make or cmake have a new target?
    • Did the requirements or the installation process change? (rare)
  • Update continuous integration server configurations if necessary (e.g. with new version requirements for each of MFEM's dependencies)
    • .github
    • .appveyor.yml
  • Update .gitignore:
    • Check if make distclean; git status shows any files that were generated from the source by the project (not an IDE) but we don't want to track in the repository.
    • Add new patterns (just for the new files above) and re-run the above test.
  • New examples:
    • All sample runs at the top of the example source file work.
    • Update examples/makefile:
      • Add the example code to the appropriate SEQ_EXAMPLES and PAR_EXAMPLES variables.
      • Add any files generated by it to the clean target.
      • Add the example binary and any files generated by it to the top-level .gitignore file.
    • Update examples/CMakeLists.txt:
      • Add the example code to the ALL_EXE_SRCS variable.
      • Make sure THIS_TEST_OPTIONS is set correctly for the new example.
    • List the new example in doc/CodeDocumentation.dox.
    • If new examples directory (e.g.examples/pumi), list it in doc/CodeDocumentation.conf.in
    • Companion pull request for documentation in mfem/web repo:
      • Update or add example-specific documentation, see e.g. the src/examples.md.
      • Add the description, labels and screenshots in src/examples.md and src/img.
      • In examples.md, list the example under the appropriate categories, add new categories if necessary.
      • Add a short description of the example in the "Extensive Examples" section of features.md.
  • New miniapps:
    • All sample runs at the top of the miniapp source file work.
    • Update top-level makefile and makefile in corresponding miniapp directory.
    • Add the miniapp binary and any files generated by it to the top-level .gitignore file.
    • Update CMake build system:
      • Update the CMakeLists.txt file in the miniapps directory, if the new miniapp is in a new directory.
      • Add/update the CMakeLists.txt file in the new miniapp directory.
      • Consider adding a new test for the new miniapp.
    • List the new miniapp in doc/CodeDocumentation.dox
    • If new miniapps directory (e.g.miniapps/nurbs), add it to MINIAPP_SUBDIRS in the makefile.
    • If new miniapps directory (e.g.miniapps/nurbs), list it in doc/CodeDocumentation.conf.in
    • Companion pull request for documentation in mfem/web repo:
      • Update or add miniapp-specific documentation, see e.g. the src/meshing.md and src/electromagnetics.md files.
      • Add the description, labels and screenshots in src/examples.md and src/img.
      • The miniapps go at the end of the page, and are usually listed only under a specific "Application (PDE)" category.
      • Add a short description of the miniapp in the "Extensive Examples" section of features.md.
  • New capability:
    • All new public, protected, and private classes, methods, data members, and functions have full Doxygen-style documentation in source comments. Documentation should include descriptions of member data, function arguments and return values, template parameters, and prerequisites for calling new functions.
    • Pointer arguments and return values must specify whether ownership is being transferred or lent with the call.
    • Any new functions should include descriptions of their intended use e.g. for internal use only, user-facing, etc., along with references to example code whenever possible/appropriate.
    • Consider adding new sample runs in existing examples to highlight the new capability.
    • Consider saving cool simulation pictures with the new capability in the Confluence gallery (LLNL only) or submitting them, via pull request, to the gallery section of the mfem/web repo.
    • If this is a major new feature, consider mentioning it in the short summary inside README (rare).
    • List major new classes in doc/CodeDocumentation.dox (rare).
  • Update this checklist, if the new pull request affects it.
  • Run make unittest to make sure all unit tests pass.
  • Run the tests in tests/scripts.
  • (LLNL only) After merging:
    • Update internal tests to include the new features.

Master/Next Workflow

MFEM uses a master/next-branch workflow as described below:

  • The master branch should always be of release quality and changes should not be merged until they have been fully tested. This branch is protected, and changes can only be made through pull requests.

  • After approval, a pull request is merged manually (by MFEM developers) in the next branch for testing and the in-next label is added to the PR. This can be done as follows:

    # Pull the latest version of the "feature-dev" branch
git checkout feature-dev
git pull

# Pull the latest version of the "next" branch
git checkout next
git pull

# Merge "feature-dev" into "next", resolving conflicts, if necessary.
# Use the "--no-ff" flag to create a new commit with merge message.
git merge --no-ff feature-dev

# Push the "next" branch to the server
git push

  • After a week of testing in next (excluding bugfixes), both on GitHub, as well as internally at LLNL, the original PR is merged into master (provided there are no issues).

  • After the merge, the feature branch is deleted (unless it is a long-term project with periodic PRs).

  • The next branch is used just for integrated testing of all PRs approved for merging into master to verify that each works individually and that all of them work as a group. This branch can be discarded at any time, though we typically do that only at the end of a release cycle.

Releases

  • Releases are just tags in the master branch, e.g. https://github.com/mfem/mfem/releases/tag/v3.3.2, and have a version that ends in an even "patch" number, e.g. v3.2.2 or v3.4 (by convention v3.4 is the same as v3.4.0.) Between releases, the version ends in an odd "patch" number, e.g. v3.3.3.

  • We use milestones to coordinate the work on different PRs toward a release, see for example the v3.3.2 release.

  • After a release is complete, the next branch is recreated, e.g. as follows (replace 3.3.2 with current release):

    • Rename the current next branch to next-pre-v3.3.2.
    • Create a new next branch starting from the v3.3.2 release.
    • Local copies of next can then be updated with git fetch origin next && git checkout -B next origin/next.

Release Checklist

  • Update the MFEM version in the following files:

    • CHANGELOG
    • makefile
    • CMakeLists.txt
    • doc/CodeDocumentation.conf.in

  • Check that version requirements for each of MFEM's dependencies are documented in INSTALL and up-to-date

  • Check that continuous integration server configurations reflect the dependency version requirements of the new release

    • .github
    • .appveyor.yml

  • Update the CHANGELOG to organize all release contributions

  • Review the whole source code once over

  • Ask MFEM-based applications to test the pre-release branch

  • Test on additional platforms and compilers

  • Tag the repository:

    git tag -a v3.1 -m "Official release v3.1"
git push origin v3.1

  • Create the release tarball and push to mfem/releases.

  • Recreate the next branch as described in previous section.

  • Update and push documentation to mfem/doxygen.

  • Update URL shortlinks:

    • Create a shortlink at http://bit.ly/ for the release tarball, e.g. https://mfem.github.io/releases/mfem-3.1.tgz.
    • (LLNL only) Add and commit the new shortlink in the links and links-mfem files of the internal mfem/downloads repo.
    • Add the new shortlinks to the MFEM packages in spack, homebrew/science, VisIt, etc.

  • Update website in mfem/web repo:

    • Update version and shortlinks in src/index.md and src/download.md.
    • Use cloc-1.62.pl and ls -lh to estimate the SLOC and the tarball size in src/download.md.

LLNL Workflow

Mirroring on Bitbucket

  • The GitHub master and next branches are mirrored to the LLNL institutional Bitbucket repository as gh-master and gh-next.

  • gh-master is merged into LLNL's internal master through pull requests; write permissions to master are restricted to ensure this is the only way in which it gets updated.

  • We never push directly from LLNL to GitHub.

  • Versions of the code on LLNL's internal server, from most to least stable:

    • MFEM official release on mfem.org -- Most stable, tested in many apps.
    • mfem:master -- Recent development version, guaranteed to work.
    • mfem:gh-master -- Stable development version, passed testing, you can use it to build your code between releases.
    • mfem:gh-next -- Bleeding-edge development version, may be broken, use at your own risk.

Mirroring on GitLab

  • MFEM repository is also mirrored on the LLNL GitLab instance, in a semi-automated manner.

  • This instance is meant to complete CI testing with tests on Livermore Computing systems. GitLab pipeline status is reported in the corresponding GitHub pull request.

  • In GitLab pipelines, TPLs (dependencies) are built using Spack, driven by Uberenv.

  • No change to the MFEM repo can be made on this instance.

Automated Testing

MFEM has several levels of automated testing running on GitHub, as well as on local Mac and Linux workstations, and Livermore Computing clusters at LLNL.

In addition, developers can set local git hooks to run some quick checks on commit or push, see the README in the config/githooks directory.

Linux and Mac smoke tests

We use GitHub Actions to drive the default tests on the master and next branches. See the .github/workflows files and the logs at https://github.com/mfem/mfem/actions.

Testing using GitHub Actions should be kept lightweight, as there is a time constraint on jobs. Two virtual machines are configured - Mac (OS X) and Linux.

  • Tests on the master branch are triggered whenever a PR is issued on this branch.
  • Tests on the next branch are currently scheduled to run each night.

Windows smoke test

We use Appveyor to test building with the MS Visual C++ compiler in a Windows environment, as well as to test the CMake build. See the .appveyor file and the build logs at https://ci.appveyor.com/project/mfem/mfem.

CMake is used to generate the MSVC Project files and drive the build. A release and debug build is performed with a simple run of ex1 to verify the executable.

Tests at LLNL

  • We mirror the master and next branches internally (to gh-master and gh-next) and run longer nightly tests via cron. On the weekends, a more extensive test is run which extracts and executes all the different sample runs from each example.

  • We also mirror PRs on the LLNL GitLab instance. PR mirroring can only be triggered by LLNL developers, but test status is publicly available. Only LLNL developers can access the detailed test report.

Contact Information

  • Contact the MFEM team by posting to the GitHub issue tracker. Please perform a search to make sure your question has not been answered already.

  • Email communications should be sent to the MFEM developers mailing list, [email protected].

Developer's Certificate of Origin 1.1

By making a contribution to this project, I certify that:

(a) The contribution was created in whole or in part by me and I have the right to submit it under the open source license indicated in the file; or

(b) The contribution is based upon previous work that, to the best of my knowledge, is covered under an appropriate open source license and I have the right under that license to submit that work with modifications, whether created in whole or in part by me, under the same open source license (unless I am permitted to submit under a different license), as indicated in the file; or

(c) The contribution was provided directly to me by some other person who certified (a), (b) or (c) and I have not modified it.

(d) I understand and agree that this project and the contribution are public and that a record of the contribution (including all personal information I submit with it, including my sign-off) is maintained indefinitely and may be redistributed consistent with this project or the open source license(s) involved.