Contributing to PETSc

As you gain experience in building, using, and debugging with PETSc, you may become able to contribute!

Before contributing code to PETSc, please read the PETSc Style and Usage Guide. You may also be interested to read about The Design of PETSc.

See Getting your code and documentation into PETSc for how to submit merge requests. Note that this requires you to use Git.

Once you have gained experience with developing PETSc source code and submitted merge requests, you can become an active member of our development and push changes directly to the petsc repository. Send mail to petsc-maint@mcs.anl.gov to arrange it.

How-tos

Some of the source code is documented to provide direct examples/templates for common contributions, adding new implementations for solver components:

Documentation fixes

We welcome corrections for our documentation. You can submit corrections to petsc-maint@mcs.anl.gov or post an issue. Add the label “docs”. You can also supply corrections to many web pages directly by clicking “Edit this page”, making your edits, following the instructions to make a merge request, and following the integration process.

Browsing Source

One can browse the development repositories at the following location

Obtaining the development version of PETSc

Install Git if it is not already installed on your machine, then obtain PETSc with the following:

$ git clone https://gitlab.com/petsc/petsc.git
$ cd petsc

PETSc can now be configured in the usual way, specified on the Installation page

To update your copy of PETSc

$ git pull

Once updated, you will usually want to rebuild completely

$ make reconfigure all

This is a shorthand version of

$ $PETSC_DIR/$PETSC_ARCH/lib/petsc/conf/reconfigure-$PETSC_ARCH.py && make all

If you absolutely cannot use Git then you can access tarballs directly, as in Other ways to obtain PETSc.

Git instructions

We provide some information on common operations, here, but to contribute you are expected to know the basics of Git usage, for example from git help, man git, or the Git book.

Setting up Git

First, set up your Git environment to establish your identity.

To stay oriented when working with branches, we encourage configuring git-prompt.

To get tab-completion for Git commands, one can download and then source git-completion.bash.

Starting a new feature branch

  • Obtain the PETSc source.

    • If you have write access to the PETSc GitLab repository, use git clone git@gitlab.com/petsc/petsc (or just use a clone you already have).

    • Otherwise, Create a fork (your own copy of the PETSc repository).

      • You will be asked to “Select a namespace to fork the project”; click the green “Select” button.

      • If you already have a clone on your machine of the PETSc repository you would like to reuse

        $ git remote set-url origin git@gitlab.com:YOURGITLABUSERNAME/petsc.git
        

        and otherwise

        $ git clone git@gitlab.com:YOURGITLABUSERNAME/petsc.git
        
  • Determine the appropriate integration branch to start from (usually main).

  • Create and switch to a new feature branch:

    $ git fetch
    $ git checkout -b <loginname>/<affected-package>-<short-description> origin/main  # or origin/release
    

    For example, Barry’s new feature branch on removing CPP in snes/ will use

    $ git checkout -b barry/snes-removecpp origin/main``
    

    Use all lowercase and no additional underscores.

  • Write code and tests.

  • Inspect changes and stage code using standard Git commands, e.g.

    $ git status
    $ git add file1 file2
    $ git commit
    
  • Commit code with good commit messages.

    $ git commit
    
  • Create a clean commit history.

  • Push the feature branch to the remote repository:

    % git push -u origin barry/snes-removecpp
    
  • Once the branch is ready for submission, see Getting your code and documentation into PETSc.

Writing commit messages

ComponentName: one-line explanation of commit

After a blank line, write a more detailed explanation of the commit.
Many tools do not auto-wrap this part, so wrap paragraph text at a
reasonable length. Commit messages are meant for other people to read,
possibly months or years later, so describe the rationale for the change
in a manner that will make sense later, and which will be provide helpful
search terms.

Use the imperative, e.g. "Fix bug", not "Fixed bug".

If any interfaces have changed, the commit should fix occurrences in
PETSc itself and the message should state its impact on users.

We have defined several standard commit message tags you should use; this makes it easy
to search for specific types of contributions. Multiple tags may be used
in the same commit message.

\spend 1h or 30m

* If other people contributed significantly to a commit, perhaps by
reporting bugs or by writing an initial version of the patch,
acknowledge them using tags at the end of the commit message.

Reported-by: Helpful User <helpful@example.com>
Based-on-patch-by: Original Idea <original@example.com>
Thanks-to: Incremental Improver <improver@example.com>

* If work is done for a particular well defined funding
source or project you should label the commit with one
or more of the tags

Funded-by: My funding source
Project: My project name

Creating a clean commit history

Often a branch’s commit history does not present a logical series of changes. Extra commits from bug-fixes or tiny improvements may accumulate. One commit may contain multiple orthogonal changes. The order of changes may be incorrect. Branches without a clean commit history will often break git bisect.

Ideally, each commit in a submitted branch will allow PETSc to build, compile, and pass its tests, while presenting a small-as-possible set of very closely related changes. However, especially prioritize rewriting to avoid commits which change the content of previous commits, as this makes reviewing on a per-commit basis difficult.

Rewriting history can be done in several ways; the easiest is often with the interactive rebase command, which allows one to combine (“squash”), rearrange, and edit commits.

It is better to clean up your commits regularly than to wait until you have a large number of them.

For example, if you have made three commits and the most recent two are fixes for the first, you could use

$ git rebase -i HEAD~3

If the branch has already been pushed, the rewritten branch is not compatible with the remote copy of the branch. You must force push your changes with

$ git push -f origin branch-name

to update the remote branch with your copy. This must be done with extreme care and only if you know someone else has not changed the remote copy of the branch, otherwise you will lose those changes. Never do a git pull after you rebase since that will merge the old branch into your local one and create a mess 2.

You can use git log to see the recent changes to your branch and help determine what commits should be rearranged, combined, or split. You may also find it helpful to use an additional tool such as git-gui, lazygit, or various GUI tools.

Rebasing your branch

You may also want to rebase your branch onto to the latest version of an integration branch 1, if the integration branch has had relevant changes since you started working on your feature branch.

$ git fetch origin                              # assume origin --> PETSc upstream
$ git checkout myname/component-feature
$ git branch myname/component-feature-backup-1  # optional
$ git rebase origin/main                        # or origin/release

Other ways to obtain PETSc

Getting a Tarball of the git main branch of PETSc

Use the following URL: https://gitlab.com/petsc/petsc/get/main.tar.gz

This mode is useful if you are on a machine where you cannot install Git or if it has a firewall blocking http downloads.

After the tarballs is obtained - do the following:

$ tar zxf petsc-petsc-CHANGESET.tar.gz
$ mv petsc-petsc-CHANGESET petsc

To update this copy of petsc, re-download the above tarball. The URL above gets the latest changes immediately when they are pushed to the repository.

Getting the Nightly tarball of the git main branch of PETSc

The nightly tarball will be equivalent to the release tarball - with all the documentation built. Use the following URL:

http://ftp.mcs.anl.gov/pub/petsc/petsc-main.tar.gz

To update your copy of petsc simply get a new copy of the tar file. The tar file at the ftp site is updated once each night [around midnight Chicago time] with the latest changes to the development version of PETSc.

Footnotes

1

Rebasing is generally preferable to merging an upstream branch.

2

You may wish to make it impossible to perform these usually-undesired “non fast-forward” merges when pulling, with git config --global pull.ff only.