GitLab CI Pipeline Execution
============================
The repository contains DockerFiles and GitLab Runner configuration
files to support automated testing and documentation builds.
General information on configuring GitLab CI pipelines can be found
in the official `Gitlab documentation <https://docs.gitlab.com/ee/ci/yaml/>`_.
The GitLab CI configuration entry point is the :file:`.gitlab-ci.yml` file
at the root of the source tree.
Configuration templates are found in the files in the
:file:`admin/ci-templates/` directory.
Docker images used by GitLab Runner are available on `Docker Hub <https://hub.docker.com/u/gromacs>`__.
Images are (re)built manually using details in :file:`admin/containers`.
This documentation is incomplete, pending resolution of :issue:`3275`.
.. todo:: Expand this documentation to resolve :issue:`3275`
.. todo:: Discuss the distinct characteristics of |Gromacs| CI pipelines to relevant to job configuration.
(:issue:`3472` and :issue:`3617`)
.. todo:: (:issue:`3472` and :issue:`3617`) Comment on the number of pipelines that can be or which are likely to be running at the same time.
(:issue:`3472` and :issue:`3617`)
.. note::
Full automated testing is only available for merge requests originating from
branches of the main https://gitlab.com/gromacs/gromacs repository.
GitLab CI pipelines created for forked repositories will include fewer jobs
in the testing pipeline. Non-trivial merge requests may need to be issued
from a branch in the ``gromacs`` project namespace in order to receive
sufficient testing before acceptance.
Configuration files
-------------------
At the root of the repository, :file:`.gitlab-ci.yml` defines the stages and
some default parameters, then includes files from :file:`admin/gitlab-ci/` to
define jobs to be executed in the pipelines.
Note that job names beginning with a period (``.``) are
`"hidden" <https://docs.gitlab.com/ee/ci/yaml/#hidden-keys-jobs>`_.
Such jobs are not directly eligible to run, but may be used as templates
via the `*extends* job property <https://docs.gitlab.com/ee/ci/yaml/#extends>`_.
Job parameters
--------------
Refer to https://docs.gitlab.com/ee/ci/yaml for complete documentation on
GitLab CI job parameters, but note the following GROMACS-specific conventions.
.. glossary::
before_script
Used by several of our templates to prepend shell commands to
a job *script* parameter.
Avoid using *before-script* directly, and be cautious
about nested *extends* overriding multiple *before_script* definitions.
job cache
There is no global default, but jobs that build software will likely
set *cache*. To explicitly unset *cache* directives, specify a job
parameter of ``cache: {}``.
Refer to `GitLab docs <https://docs.gitlab.com/ee/ci/yaml/#cache>`__
for details. In particular, note the details of cache identity according
to `cache:key <https://docs.gitlab.com/ee/ci/yaml/#cachekey>`__
image
See :doc:`/dev-manual/containers` for more about the Docker images used for the
CI pipelines. If a job depends on artifacts from previous jobs, be sure
to use the same (or a compatible) image as the dependency!
rules
only
except
when
*Job* parameters for controlling the circumstances under which jobs run.
(Some key words may have different meanings when occurring as elements
of other parameters, such as *archive:when*, to which this note is not
intended to apply.)
Instead of setting any of these directly in a job definition, try to use
one of the pre-defined behaviors (defined as ``.rules:<something>`` in
:file:`admin/gitlab-ci/rules.gitlab-ci.yml`).
Errors or unexpected behavior will occur if you specify more than one
*.rules:...* template, or if you use these parameters in combination
with a *.rules...* template.
To reduce errors and unexpected behavior, restrict usage of these controls
to regular job definitions (don't use in "hidden" or parent jobs).
Note that *rules* is not compatible with the older *only* and *except*
parameters. We have standardized on the (newer) *rules* mechanism.
tags
Jobs that can only run in the |Gromacs| GitLab CI Runner infrastructure
should require the ``k8s-scilifelab`` tag.
These include jobs that specify Kubernetes configuration variables or
require special facilities, such as GPUs or MPI.
Note that the *tag* controls which Runners are eligible to take a job.
It does not affect whether the job is eligible for addition to a particular pipeline.
Additional *rules* logic should be used to make sure that jobs with the
``k8s-scilifelab`` do not become eligible for pipelines launched outside
of the |Gromacs| project environment.
See, for instance, :term:`CI_PROJECT_NAMESPACE`
variables
Many job definitions will add or override keys in *variables*.
Refer to `GitLab <https://docs.gitlab.com/ee/ci/yaml/#variables>`__
for details of the merging behavior. Refer to :ref:`variables` for local usage.
Schedules and triggers
----------------------
Pipeline `schedules <https://gitlab.com/help/ci/pipelines/schedules>`__ are
configured through the GitLab web interface.
Scheduled pipelines may provide different variable definitions through the
environment to jobs that run under the ``schedules``
`condition <https://gitlab.com/help/ci/pipelines/schedules#using-only-and-except>`__.
Nightly scheduled pipelines run against ``master`` and *release* branches in
the GROMACS repository.
Running post-merge-acceptance pipelines
"""""""""""""""""""""""""""""""""""""""
The Gitlab CI for |Gromacs| runs a set of jobs by default only after a MR has been
accepted and the resulting commit is included in the target branch if it is ``master``
or one of the *release* branches. Those jobs can be triggered manually using the
``POST_MERGE_ACCEPTANCE`` input variable documented below when executing a new pipeline
through the Gitlab web interface.
Global templates
----------------
In addition to the templates in the main job definition files,
common "mix-in" functionality and behavioral templates are defined in
:file:`admin/gitlab-ci/global.gitlab-ci.yml`.
For readability, some parameters may be separated into their own files, named
according to the parameter (e.g. :file:`rules.gitlab-ci.yml`).
Jobs beginning with ``.use-`` provide mix-in behavior, such as boilerplate for
jobs using a particular tool chain.
Jobs beginning with a `parameter <https://docs.gitlab.com/ee/ci/yaml>`__
name allow parameters to be set in a single place for common job characteristics.
If providing more than a default parameter value, the job name should be suffixed
by a meaningful descriptor and documented within
:file:`admin/gitlab-ci/global.gitlab-ci.yml`
Job names
---------
Job names should
1. Indicate the purpose of the job.
2. Indicate relationships between multi-stage tasks.
3. Distinguish jobs in the same stage.
4. Distinguish job definitions throughout the configuration.
Jobs may be reassigned to different stages over time, so including the stage
name in the job name is not helpful, generally. If tags like "pre" and "post,"
or "build" and "test" are necessary to distinguish phases of, say, "webpage,"
then such tags can be buried at the end of the job name.
Stylistically, it is helpful to use delimiters like ``:`` to distinguish the
basic job name from qualifiers or details. Also consider
`grouping jobs <https://docs.gitlab.com/ee/ci/pipelines/index.html#grouping-jobs>`__
.. _variables:
Updating regression tests
-------------------------
Changes in |Gromacs| that require changes in regression-tests are notoriously hard,
because a merge request that tests against the non-updated version of the
regression tests will necessarily fail, while updating regression tests while
the current change is not integrated into master, might cause other
merge request pipelines to fail.
The solution is a new regression-test branch or commit, uploaded to gitlab.
Then set that regression test branch with REGRESSIONTESTBRANCH or
the specific commit with REGRESSIONTESTCOMMIT when
running the specific pipeline that requires the regressiontest-update.
See below on how to set variables for specific pipelines.
Variables
---------
The GitLab CI framework, GitLab Runner, plugins, and our own scripts set and
use several `variables <https://docs.gitlab.com/ee/ci/variables/README.html>`__.
Default values are available from the ``.variables:default`` definition in
:file:`admin/gitlab-ci/global.gitlab-ci.yml`.
Many of the mix-in / template jobs provide additional or overriding definitions.
Other variables may be set when making final job definitions.
Variables may control the behvior of GitLab-CI (those beginning with ``CI_``),
GitLab Runner and supporting infrastructure, or may be used by job definitions,
or passed along to the environment of executed commands.
*variables* keys beginning with ``KUBERNETES_`` relate to the GitLab Runner
`Kubernets executor <https://docs.gitlab.com/runner/executors/kubernetes.html#the-kubernetes-executor>`__
Other important variable keys are as follows.
.. glossary::
CI_PROJECT_NAMESPACE
Distinguishes pipelines created for repositories in the ``gromacs``
GitLab project space. May be used to pre-screen jobs to determine
whether |Gromacs| GitLab infrastructure is available to the pipeline
before the job is created.
COMPILER_MAJOR_VERSION
Integer version number provided by toolchain mix-in for convenience and
internal use.
CMAKE
``gromacs/ci-...`` Docker images built after October 2020 have several
versions of CMake installed. The most recent version of CMake in the
container will be appear first in ``PATH``. To allow individual jobs to
use specific versions of CMake, please write the job *script* sections
using ``$CMAKE`` instead of ``cmake`` and begin the *script* section with
a line such as ``- CMAKE=${CMAKE:-$(which cmake)}``. Specify a CMake
version by setting the *CMAKE* variable to the full executable path for
the CMake version you would like to use. See also :doc:`containers`.
CMAKE_COMPILER_SCRIPT
CMake command line options for a tool chain. A definition is provided by
the mix-in toolchain definitions (e.g. ``.use-gcc8``) to be appended to
:command:`cmake` calls in a job's *script*.
CMAKE_MPI_OPTIONS
Provide CMake command line arguments to define GROMACS MPI build options.
GROMACS_MAJOR_VERSION
Read-only environment variable for CI scripts to check the
library API version to expect from the ``build`` job artifacts.
Initially, this variable is only defined in
:file:`admin/gitlab-ci/api-client.matrix/gromacs-master.gitlab-ci.yml`
but could be moved to :file:`admin/gitlab-ci/global.gitlab-ci.yml` if found
to be of general utility.
GROMACS_RELEASE
Read-only environment variable that can be checked to see if a job is
executing in a pipeline for preparing a tagged release.
Can be set when launching pipelines via the GitLab web interface.
For example, see *rules* mix-ins in :file:`admin/gitlab-ci/global.gitlab-ci.yml`.
EXTRA_INSTALLS
List additional OS package requirements. Used in *before_script* for some
mix-in job definitions to install additional software dependencies. If
using such a job with *extends*, override this variable key with a
space-delimited list of packages (default: ``""``). Consider proposing a
patch to the base Docker images to include the dependency to reduce
pipeline execution time.
REGRESSIONTESTBRANCH
Use this branch of the regressiontests rather than master to allow for
merge requests that require updated regression tests with valid CI tests.
REGRESSIONTESTCOMMIT
Use this commit to the regressiontests rather than the head on master to
allow for merge requests that require updated regression tests with
valid CI tests.
POST_MERGE_ACCEPTANCE
Read-only environment variable that indicates that only jobs scheduled to
run after a commit has been merged into its target branch should be executed.
Can be set to run pipelines through the web interface or as schedules.
For use please see the *rules* mix-ins in :file:`admin/gitlab-ci/global.gitlab-ci.yml`.
.. todo:: Define common variables.
``BUILD_DIR``, ``INSTALL_DIR``, ``CACHE_FALLBACK_KEY``, ...
Setting variables
-----------------
Variables for individual piplelines are set in the gitlab interface under
``CI/CD``; ``Pipelines``. Then chose in the top right corner ``Run Piplelines``.
Under ``Run for``, the desired branch may be selected, and variables may be set
in the fields below.