GROMACS change management

This documentation assumes the reader is already familiary with using git for managing file revisions.

Getting started

  1. Go to
  2. Click Register (you can choose any OpenID provider including any existing Google/Yahoo account. If you manually enter the URL make sure to start with http(s)://)
  3. Choose a username and add an ssh key

See here for a quick intro into Gerrit.

Creating the SSH key for Gerrit

In order to push your commits to gerrit server, you must have an SSH key in your computer which matches with the one registered in your Gerrit user account. To do so, you first need to create this unique SSH key. You will be asked to enter a passphrase. This is optional with respect to Gerrit, but it is a good security practice to have it.

To proceed with the creation of the SSH key, type the following commands from your terminal window:

$ cd ~/.ssh

$ ssh-keygen -t rsa -C ""

Please substitute the email string in the command above with the same email address which you used to register the account in Gerrit.

Now you have created your public SSH key, which you need to copy/paste into your Gerrit profile. First, open it with the following command:

$ cat

Copy all the contents of the file in your clipboard, and switch to your favorite web browser where you logged in to Gerrit GROMACS page. Click on your username at the top right corner of the Gerrit webpage and select “Settings”. You should now be in your Gerrit profile settings page, where you should see a vertical menu.

From this vertical menu, select “SSH Public Keys”, then click the button “Add Key …” and an edit box will appear below the button. Here you need to paste the contents of file, which you previously copied to your clipboard.

Now you are ready to operate!

Setting up a local repository to work with gerrit

Either clone using:

$ git clone ssh://

(replace USER with your username)

or change the remote url using:

$ git remote set-url origin ssh://

(change USER with the username you’ve registered)

Or add a new remote url using:

$ git remote add upload ssh://

If you are working with a GROMACS repository other than the source code, then you should substitute e.g. regressiontests.git or releng.git instead of gromacs.git above.

Be sure to configure your user name and e-mail to match those registered to Gerrit:

git config [--global] "Your Name"
git config [--global] ""

It is optional if you want to set those settings for git on a global level, or just for the current repository.

If necessary, register the e-mail address you want to use with Gerrit.

Install the commit hook

Differently from a simple usage of git, with Gerrit a Change-ID is needed at the end of each commit message. Gerrit uses Change-IDs to understand whether your new commit is patching a previous commit or it should be regarded as a separate, different patch, uncorrelated with your previously pushed commits.

To allow git to append such Change-IDs automatically after each commit, type the following command:

$ scp -p .git/hooks/

(change USER with the username you’ve registered in Gerrit)


This commit hook needs to be added to the repo where the commit will occur, not the repo where the push to upstream will occur (should they be different).

Uploading a commit for review

Make sure your HEAD is up to date (use git pull --rebase origin if someone else has committed since you last pulled), check that your commit message follows the Guidelines for formatting of git commits, make your commit and then use

$ git push origin HEAD:refs/for/BRANCH

Replace BRANCH with the branch it should be committed to. Master has a number of sub branches that can be used to show what the patch is relevant to such as OpenCL and tools-cleanup. These can be pushed to by specifying them after the branch, for example BRANCH/domdec-cleanup.

When updating/replacing an existing change, make sure the commit message has the same Change-ID. Please see the section Ammending a change <gmx-ammend-change> below.

Uploading a draft commit for review

Uploading a draft lets you share a change which isn’t ready yet for review for merging. It is only visible to those people you invite as reviewers, which you need to add explicitly. You upload a change as a draft by uploading it to refs/drafts/branch instead of refs/for/branch. Typically you want to push to refs/drafts/master.

Jenkins is not automatically triggered for drafts, but if you add “Jenkins Buildbot” as a reviewer, it learns that you might be interested in having it try out your code. Then, you can go to Jenkins and log in with your OpenID. Then go to and tell it to search for the commit for which you want to trigger the build agents. For example, is 1238 (but maybe SHA or ChangeID will work, too).

After uploading a commit


$ git reset --keep HEAD^

to reset your branch to the HEAD before the commit you just uploaded. This allows you to keep your repo in sync with what every other repo thinks is the HEAD. In particular, if you have another patch to upload (or worse, have to pull in other people’s patches, and then have a new patch), you probably do not want to have the second patch depend on the first one. If the first one is rejected, you have made extra work for yourself sorting out the mess. Your repo still knows about the commit, and you can cherry-pick it to somewhere if you want to use it.

Code Review

Reviewing someone else’s uploaded commit

The reviewing workflow is the following:

  1. shows all open changes
  2. A change needs a +2 and usually +1 review, as well as a +2 verified to be allowed to be merged.
  3. Usually a patch goes through several cycles of voting, commenting and updating before it becomes merged, with votes from the developers indicating if they think that change hat progressed enough to be included.
  4. A change is submitted for merging and post-submit testing by clicking “Submit” by one of the main developers. This should be done by the reviewer after voting +2. After a patch is submitted it is replicated to the main git server.

Do not review your own code. The point of the policy is that at least two non-authors have voted +1, and that the issues are resolved in the opinion of the person who applies a +2 before a merge. If you have uploaded a minor fix to someone else’s patch, use your judgement in whether to vote on the patch +1.

Guide for reviewing

  • First and foremost, check correctness to the extent possible;
  • As portability and performance are the most important things (after correctness) do check for potential issues;
  • Check adherence to the GROMACS coding standards;
  • We should try to ensure that commits that implement bugfixes (as well as important features and tasks) get a Redmine entry created and linked. The linking is done automatically by Redmine if the commit message contains keyword “#issueID”, the valid syntax is explained below.
  • If the commit is a bugfix:
    • if present in Redmine it has to contain a valid reference to the issue;
    • if it’s a major bug, there has to be a bug report filed in Redmine  (with urgent or immediate priority) and referenced appropriately.
  • If the commit is a feature/task implementation:
    • if it’s present in Redmine it has to contain a valid reference to the issue;
    • If no current issue is currently present and the change would benefit of one for future explanation on why it was added, a new redmine issue should be created.

Use of Verify

Jenkins has been installed for automated build testing. So it isn’t required to vote “verify +2” anymore. As the testing is not always perfect, and because test coverage can be spotty, developers can still manually vote to indicate that a change performs as intended. Please note that this should not be abused to bypass Jenkins testing. The vote from the test suite should only be discarded if failures are caused by unrelated issues.

Further information

Currently it is possible to review your own code. It is undesirable to review your own code, because that defeats the point. It will be deactivated if it is being abused and those responsible may lose their voting rights.

For further documentation:


How do I access gerrit behind a proxy?

If you are behind a firewall blocking port 22, you can use socat to overcome this problem by adding the following block to your ~/.ssh/config

       User USER
       ProxyCommand socat -,proxyport=PORT

Replace YOURPROXY, PORT and USER, (but not PROXY!) with your own settings.

How can I submit conflicting changes?

When there are several, mutually conflicting changes in gerrit pending for review, the submission of the 2nd and subsequent ones will fail. Those need to be resolved locally and updated by

$ git pull --rebase

Then fix the conflicts and use

$ git push

Please add a comment (review without voting) saying that it was rebased with/without conflicts, to help the reviewer.

How do I upload an update to a pending change?

First, obtain the code you want to update. If you haven’t changed your local repository, then you already have it. Maybe you can check out the branch again, or consult your git reflog. Otherwise, you should go to gerrit, select the latest patch set (remembering that others may have contributed to your work), and use the “Download” link to give you a “Checkout” command that you can run, e.g.

$ git fetch ssh:// refs/changes/?/?/? && git checkout FETCH_HEAD

Make your changes, then add them to the index, and use

$ git commit --amend
$ git push origin HEAD:refs/for/BRANCH

When amending the previous commit message, leave the “Change-Id” intact so that gerrit can recognize this is an update and not open a new issue.

DO NOT rebase your patch set and update it in one step. If both are done in one step, the diff between patch set versions has both kinds of changes. This makes it difficult for the reviewer, because it is not clear what parts have to be re-reviewed. If you need to update and rebase your change please do it in two steps (order doesn’t matter). gerrit has a feature that allows you to rebase within gerrit, which creates the desired independent patch for that rebase (if the rebase is clean).

How do I get a copy of my commit for which someone else has uploaded a patch?

Gerrit makes this easy. You can download the updated commit in various ways, and even copy a magic git command to your clipboard to use in your shell.

You can select the kind of git operation you want to do (cherry-pick is best if you are currently in the commit that was the parent, checkout is best if you just want to get the commit and not worry about the current state of your checked out git branch) and how you want to get it. The icon on the far right will paste the magic shell command into your clipboard, for you to paste into a terminal to use.

How do I submit lots of independent commits (e.g. bug fixes)?

Simply pushing a whole commit tree of unrelated fixes creates dependencies between them that make for trouble when one of them needs to be changed. Instead, from an up-to-date repo, create and commit the first change (or git cherry-pick it from an existing other branch). Upload it to gerrit. Then do

$ git reset --keep HEAD^

This will revert to the old HEAD, and allow you to work on a new commit that will be independent of the one you’ve already uploaded. The one you’ve uploaded won’t appear in the commit history until it’s been reviewed and accepted on gerrit and you’ve pulled from the main repo, however the version of it you uploaded still exists in your repo. You can see it with git show or git checkout using its hash - which you can get from the gerrit server or by digging in the internals of your repo.

How can I avoid needing to remember all these arcane git commands?

In your .gitconfig, having set the git remote for the gerrit repo to upload, use something like the following to make life easier:

        upload-r2018  = push origin HEAD:refs/for/release-2018
        upload-r2016  = push origin HEAD:refs/for/release-2016
        upload-master = push origin HEAD:refs/for/master
        upload-reset  = reset --keep HEAD^

How can I get my patch in gerrit to have a different parent?

Sometimes, some other patch under review is a relevant point from which to start work. For simple changes without conflicts to the previous work, you can use the Gerrit web UI to either rebase or cherry-pick the change you are working on.

If this is not possible, you can still use the canned gerrit checkouts to (say) checkout out patch 2117 and start work:

git fetch refs/changes/17/2117/2 && git checkout FETCH_HEAD

Other times you might have already uploaded a patch (e.g. patch 1 of 2145), but now see that some concurrent work makes more sense as a parent commit (e.g. patch 2 of 2117), so check it out as above, and then use the canned gerrit cherry-pick:

git fetch refs/changes/45/2145/1 && git cherry-pick FETCH_HEAD

Resolve any merge commits, check things look OK, and then upload. Because the ChangeId of 2145 hasn’t changed, and nothing about 2117 has changed, the second patch set of 2145 will reflect the state of 2145 now having 2117 as a parent.

This can also be useful for constructing a short development branch where the commits are somehow dependent, but should be separated for review purposes. This technique is useful when constructing a series of commits that will contribute to a release.

How can I revert a change back to an old patchset?

If a change accidentally gets updated or when a patchset is incorrect, you might want to revert to an older patchset. This can be done by fetching an old patchset, running git commit –amend to update the time stamp in the commit and pushing the commit back up to gerrit. Note that without the amending you will get an error from the remote telling you that there are no new changes.

How do I handle common errors

error: server certificate verification failed. CAfile…

If you try to cherry-pick a change from the server, you’ll probably get the error:

$ git fetch refs/changes/09/109/1 && git cherry-pick FETCH_HEAD
error: server certificate verification failed.
CAfile: /etc/ssl/certs/ca-certificates.crt
CRLfile: none while accessing

fatal: HTTP request failed

As explained here, the problem is with git not trusting the certificate and as a workaround one can set globally

$ git config --global --add http.sslVerify false

or prepend GIT_SSL_NO_VERIFY=1 to the command

$ GIT_SSL_NO_VERIFY=1  git fetch refs/changes/09/109/1 \
 && git cherry-pick FETCH_HEAD

Various error messages and their meanings

More git tips

Q: Are there some other useful git configuration settings?

A: If you need to work with branches that have large differences (in particular, if a lot of files have moved), it can be helpful to set

git config diff.renamelimit 5000

to increase the limit of inexact renames that Git considers. The default value is not sufficient, for example, if you need to do a merge or a cherry-pick from a release branch to master.

Q: How do I use git rebase (also git pull --rebase)?

A: Assume you have a local feature branch checked out, that it is based on master, and master has gotten new commits. You can then do

git rebase master

to move your commits on top of the newest commit in master. This will save each commit you did, and replay them on top of master. If any commit results in conflicts, you need to resolve them as usual (including marking them as resolved using git add), and then use

git rebase --continue

Note that unless you are sure about what you are doing, you should not use any commands that create or delete commits (git commit, or git checkout or git reset without paths). git rebase --continue will create the commit after conflicts have been resolved, with the original commit message (you will get a chance to edit it).

If you realize that the conflicts are too messy to resolve (or that you made a mistake that resulted in messy conflicts), you can use

git rebase --abort

to get back into the state you started from (before the original git rebase master invocation). If the rebase is already finished, and you realize you made a mistake, you can get back where you started with (use git log <my-branch>@{1} and/or git reflog <my-branch> to check that this is where you want to go)

git reset --hard <my-branch>@{1}

Q: How do I prepare several commits at once?

A: Assume I have multiple independent changes in my working tree. Use

git add [-p] [file]

to add one independent change at a time to the index. Use

git diff --cached

to check that the index contains the changes you want. You can then commit this one change:

git commit

 If you want to test that the change works, use to temporarily store away other changes, and do your testing.

git stash

If the testing fails, you can amend your existing commit with git commit --amend. After you are satisfied, you can push the commit into gerrit for review. If you stashed away your changes and you want the next change to be reviewed independently, do

git reset --hard HEAD^
git stash pop

(only do this if you pushed the previous change to gerrit, otherwise it is difficult to get the old changes back!) and repeat until each independent change is in its own commit. If you skip the git reset --hard step, you can also prepare a local feature branch from your changes.

Q: How do I edit an earlier commit?

A: If you want to edit the latest commit, you can simply do the changes and use

git commit --amend

If you want to edit some other commit, and commits after that have not changed the same lines, you can do the changes as usual and use

git commit --fixup <commit>


git commit --squash <commit>

where <commit> is the commit you want to change (the difference is that --fixup keeps the original commit message, while --squash allows you to input additional notes and then edit the original commit message during git rebase -i). You can do multiple commits in this way. You can also mix --fixup/--squash commits with normal commits. When you are done, use

git rebase -i --autosquash <base-branch>

to merge the --fixup/--squash commits to the commits they amend. See separate question on git rebase -i on how to choose <base-branch>.

In this kind of workflow, you should try to avoid to change the same lines in multiple commits (except in --fixup/--squash commits), but if you have already changed some lines and want to edit an earlier commit, you can use

git rebase -i <base-branch>

but you likely need to resolve some conflicts later. See git rebase -i question later.

Q: How do I split a commit?

A: The instructions below apply to splitting the HEAD commit; see above how to use git rebase -i to get an earlier commit as HEAD to split it.

The simplest case is if you want to split a commit A into a chain A’-B-C, where A’ is the first new commit, and contains most of the original commit, including the commit message. Then you can do

git reset -p HEAD^ [-- <paths>]
git commit --amend

to selectively remove parts from commit A, but leave them in your working tree. Then you can create one or more commits of the remaining changes as described in other tips.

If you want to split a commit A into a chain where the original commit message is reused for something else than the first commit (e.g., B-A’-C), then you can do

git reset HEAD^

to remove the HEAD commit, but leave everything in your working tree. Then you can create your commits as described in other tips. When you come to a point where you want to reuse the original commit message, you can use

git reflog

to find how to refer to your original commit as HEAD@{n}, and then do

git commit -c HEAD@{n}

Q: How do I use git rebase -i to only edit local commits?

A: Assume that you have a local feature branch checked out, this branch has three commits, and that it is based on master. Further, assume that master has gotten a few more commits after you branched off. If you want to use git rebase -i to edit your feature branch (see above), you probably want to do

git rebase -i HEAD~3

followed by a separate

git rebase master

The first command allows you to edit your local branch without getting conflicts from changes in master. The latter allows you to resolve those conflicts in a separate rebase run. If you feel brave enough, you can also do both at the same time using

git rebase -i master

Interacting with Gerrit

This section is intended for using git to interact with gerrit; interacting with the web UI may be better dealt with on a separate page.

Q: How do I move a change from a branch to another?

A: Moving one or a few changes is most easily done using git cherry-pick. To move a single change, first do

git checkout <target-branch>

Then, open the change/patch set in Gerrit that you want to move, select “cherry-pick” in the Download section for that patch set, and copy/paste the given command:

git fetch ... refs/changes/... && git cherry-pick FETCH_HEAD

Resolve any conflicts and do

git commit [-a]

You can also cherry-pick multiple changes this way to move a small topic branch. Before pushing the change to Gerrit, remove the lines about conflicts from the commit message, as they don’t serve any useful purpose in the history. You can type that information into the change as a Gerrit comment if it helps the review process. Note that Gerrit creates a new change for the target branch, even if Change-Ids are same in the commits. You need to manually abandon the change in the wrong branch.