# Understanding Jenkins builds¶

This page documents what different Jenkins builds actually run from the GROMACS source tree. The purpose is two-fold:

• Provide information on how to interpret Jenkins failures and how to run the same tasks locally to diagnose issues (in most cases, referring to the special targets described in Build system overview).
• Provide information on what changes in the build system (or other parts of the repository) need special care to not break Jenkins builds.

## Pre-submit verification¶

The following builds are triggered for each patch set uploaded to Gerrit.

### Compilation and tests¶

The main build compiles GROMACS with different configurations and runs the tests. The configurations used for Jenkins verification are specified in admin/builds/pre-submit-matrix.txt.

The exact build sequence can be found in admin/builds/gromacs.py, including the logic that translates the build options in the matrix file to CMake options.

### Documentation¶

This build builds various types of documentation:

• PDF reference manual using LaTeX
• Doxygen documentation extracted from the source code
• Set of HTML pages containing an installation guide, a user guide, and a developer guide, as well as links to the above. This set of HTML pages can be browsed from Jenkins.
• Man pages
• INSTALL text file

The last three require building the gmx binary and running it, so compilation failures will also show in this build. All log files that contain warnings are archived as artifacts in the build, and presence of any warnings marks the build unstable. Brief description of which part failed is reported back to Gerrit.

Additionally, the build runs some source code checks that rely on the Doxygen documentation. See the description of the check-source target in Source tree checker scripts.

Using Doxygen provides general guidelines for Doxygen usage, which can be helpful in understanding and solving Doxygen warnings and some of the check-source issues. Guidelines for #include directives provides guidelines for #include order and style, which is another part of check-source checks.

The exact build sequence is in admin/builds/documentation.py. See that file for details of what it exactly builds and how. Most changes in the documentation build system will require changes in this script, but Jenkins configuration should be more static.

### clang static analysis¶

The file admin/builds/clang-analyzer.py specifies the exact build sequence and the CMake cache variables used for clang static analysis. This file also specifies the clang version used for the analysis, as well as the C++ compiler used (clang-static-analyzer-<version>).

To run the analysis outside Jenkins, you should run both cmake and make under scan-build command using the same CMake cache variables as in the build script. When you do the initial CMake configuration with scan-build, it sets the C++ compiler to the analyzer. Note that using scan-build like this will also analyze C code, but Jenkins ignores C code for analysis. This can result in extra warnings, which can be suppressed by manually setting CMAKE_C_COMPILER to a value other than Clang static analyzer.

### uncrustify¶

This build checks for source code formatting issues with uncrustify, and enforces the copyright style. See Guidelines for code formatting for the guidelines that are enforced.

The exact build sequence is in admin/builds/uncrustify.py, which essentially just runs

admin/uncrustify.sh check --rev=HEAD^


If the any changes are required, the build is marked unstable. If the script completely fails (should be rare), the build fails. A file with issues found by the script is archived as an artifact in the build, and a summary is reported back to Gerrit (or the actual issues if there are only a few). See Automatic source code formatting for more details on code-formatting tools and on scripts to run them.

### clang-format¶

This build checks and enforces code formatting, e.g., indentation. Also, a second part of the build enforces the source code formatting. As above, see Guidelines for code formatting for the style guidelines.

The build runs according to admin/builds/clang-format.py, resulting in running

admin/clang-format.sh check --rev=HEAD^


The build is marked unstable if the code formatting resulted in any changes to the source code.

## On-demand builds¶

These builds can be triggered on request for certain changes in Gerrit, or manually from Jenkins. See Triggering builds on Gitlab for details on how to trigger these.

### Coverage¶

This build compiles one configuration of GROMACS with instrumentation for coverage, runs the tests, and produces a coverage report using gcovr. The report can be browsed on Jenkins.

The exact build sequence is in admin/builds/coverage.py, including specification of the configuration tested.

### Source tarball¶

This build creates the source tarball for distribution. Some of the content that is put into the tarball is generated by executing the gmx binary, so this build also compiles the source code (with a minimal set of options).

The build compiles the code and those targets that generate content necessary for the tarball, followed by building the package_source target. After that, it just generates a file that is used by other builds.

The exact build sequence is in admin/builds/source-package.py.

### Release workflow¶

This build creates source and regressiontest tarballs, builds, installs, and tests a few configuration using those, and builds documentation to be placed on the documentation web site for a new release. The set of configurations tested is specified in admin/builds/release-matrix.txt.

The exact build sequence is desribed in Release engineering with Gitlab. The build uses the source tarball build as a subbuild, and parts of the build are executed using admin/builds/gromacs.py and admin/builds/documentation.py.

admin/builds/get-version-info.py is used for getting the version information from the source tree as part of this workflow.

admin/builds/update-regtest-hash.py has logic to update the regressiontests tarball MD5 sum for the released tarball automatically.

### Updating regressiontests data¶

Sometimes we add new tests to the regressiontests repository. Also, as the source code or data files change, it is sometimes necessary to update regressiontests. This requires a particular CMake build type and both a single and double-precision build of GROMACS to generate all the data. Jenkins can automate much of the tedium here.

• Upload a regressiontests change that lacks the relevant reference data (either because you deleted the outdated data, or because the test is new). Jenkins will do the normal thing, which we ignore. There is now a Gerrit patch number for that change, symbolized here with MMMM.

• Go to change MMMM on gerrit, select the patch set you want to update with new reference data (usually the latest one), and comment

[JENKINS] Update

to update against the HEAD of the matching source-code branch, or

[JENKINS] Cross-verify NNNN update

to update from builds of GROMACS from the latest version of Gerrit source-code patch NNNN. You will need to do this when functionality changes in NNNN affect either the layout of the files in the reference data, or the results of the simulation, or the results of the subsequent analysis.

• Eventually, Jenkins will upload a new version of the regressiontests patch to Gerrit, which will contain the updated regressiontest data. That upload will again trigger Jenkins to do the normal pre-submit verify, which will now pass (but perhaps will only pass under cross-verify with patch NNNN, as above).

• Later, if you later need to verify an updated version of source-code patch NNNN against the newly generated reference data, go to the source-code patch NNNN and comment

[JENKINS] Cross-verify MMMM