3.12. Development build options — LAMMPS documentation

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# 3.12. Development build options

The build procedures in LAMMPS offers a few extra options which are useful during development, testing or debugging.

## 3.12.1. Monitor compilation flags (CMake only)

Sometimes it is necessary to verify the complete sequence of compilation flags generated by the CMake build. To enable a more verbose output during compilation you can use the following option.

    -D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes

Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:

    make VERBOSE=1

## 3.12.2. Report missing and unneeded ‘#include’ statements (CMake only)

The conventions for how and when to use and order include statements in LAMMPS are documented in LAMMPS programming style. To assist with following these conventions one can use the Include What You Use tool. This tool is still under development and for large and complex projects like LAMMPS there are some false positives, so suggested changes need to be verified manually. It is recommended to use at least version 0.16, which has much fewer incorrect reports than earlier versions. To install the IWYU toolkit, you need to have the clang compiler and its development package installed. Download the IWYU version that matches the version of the clang compiler, configure, build, and install it.

The necessary steps to generate the report can be enabled via a CMake variable during CMake configuration.

    -D ENABLE_IWYU=value    # value = no (default) or yes

This will check if the required binary (include-what-you-use or iwyu) and python script script (iwyu-tool or iwyu_tool or iwyu_tool.py) can be found in the path. The analysis can then be started with:

    make iwyu

This may first run some compilation, as the analysis is dependent on recording all commands required to do the compilation.

## 3.12.3. Address, Leak, Undefined Behavior, and Thread Sanitizer Support (CMake only)

Compilers such as GCC and Clang support generating instrumented binaries which use different sanitizer libraries to detect problems in the code during run-time. They can detect issues like:

> - memory leaks

> - undefined behavior

> - data races

Please note that this kind of instrumentation usually comes with a performance hit (but much less than using tools like Valgrind with a more low level approach). To enable these features, additional compiler flags need to be added to the compilation and linking stages. This is done through setting the `ENABLE_SANITIZER` variable during configuration. Examples:

    -D ENABLE_SANITIZER=none       # no sanitizer active (default)
    -D ENABLE_SANITIZER=address    # enable address sanitizer / memory leak checker
    -D ENABLE_SANITIZER=hwaddress  # enable hardware assisted address sanitizer / memory leak checker
    -D ENABLE_SANITIZER=leak       # enable memory leak checker (only)
    -D ENABLE_SANITIZER=undefined  # enable undefined behavior sanitizer
    -D ENABLE_SANITIZER=thread     # enable thread sanitizer

## 3.12.4. Code Coverage and Unit Testing (CMake only)

The LAMMPS code is subject to multiple levels of automated testing during development:

- Integration testing (i.e. whether the code compiles on various platforms and with a variety of compilers and settings),

- Unit testing (i.e. whether certain functions or classes of the code produce the expected results for given inputs),

- Run testing (i.e. whether selected input decks can run to completion without crashing for multiple configurations),

- Regression testing (i.e. whether selected input examples reproduce the same results over a given number of steps and operations within a given error margin).

The status of this automated testing can be viewed on https://ci.lammps.org.

The scripts and inputs for integration, run, and legacy regression testing are maintained in a separate repository of the LAMMPS project on GitHub. A few tests are also run as GitHub Actions and their configuration files are in the `.github/workflows/` folder of the LAMMPS git tree.

Regression tests can also be performed locally with the regression tester tool. The tool checks if a given LAMMPS binary run with selected input examples produces thermo output that is consistent with the provided log files. The script can be run in one pass over all available input files, but it can also first create multiple lists of inputs or folders that can then be run with multiple workers concurrently to speed things up. Another mode allows to do a quick check of inputs that contain commands that have changes in the current checkout branch relative to a git branch. This works similar to the two pass mode, but will select only shorter runs and no more than 100 inputs that are chosen randomly. This ensures that this test runs significantly faster compared to the full test run. These test runs can also be performed with instrumented LAMMPS binaries (see previous section).

The unit testing facility is integrated into the CMake build process of the LAMMPS source code distribution itself. It can be enabled by setting `-D ENABLE_TESTING=on` during the CMake configuration step. It requires the YAML library and matching development headers to compile (if those are not found locally a recent version of that library will be downloaded and compiled along with LAMMPS and the test programs) and will download and compile a specific version of the GoogleTest C++ test framework that is used to implement the tests. Those unit tests may be combined with memory access and leak checking with valgrind (see below for how to enable it). In that case, running so-called death tests will create a lot of false positives and thus they can be disabled by configuring compilation with the additional setting `-D SKIP_DEATH_TESTS=on`.

Software version and LAMMPS configuration requirements

The compiler and library version requirements for the testing framework are more strict than for the main part of LAMMPS. For example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x (version 4.8.x) are not sufficient. The CMake configuration will try to detect incompatible versions and either skip incompatible tests or stop with an error. Also the number of available tests will depend on installed LAMMPS packages, development environment, operating system, and configuration settings.

After compilation is complete, the unit testing is started in the build folder using the `ctest` command, which is part of the CMake software. The output of this command will be looking something like this:

       $ ctest
       Test project /home/akohlmey/compile/lammps/build-testing
            Start   1: RunLammps
      1/563 Test   #1: RunLammps ..................................   Passed    0.28 sec
            Start   2: HelpMessage
      2/563 Test   #2: HelpMessage ................................   Passed    0.06 sec
            Start   3: InvalidFlag
      3/563 Test   #3: InvalidFlag ................................   Passed    0.06 sec
            Start   4: Tokenizer
      4/563 Test   #4: Tokenizer ..................................   Passed    0.05 sec
            Start   5: MemPool
      5/563 Test   #5: MemPool ....................................   Passed    0.05 sec
            Start   6: ArgUtils
      6/563 Test   #6: ArgUtils ...................................   Passed    0.05 sec
          [...]
            Start 561: ImproperStyle:zero
    561/563 Test #561: ImproperStyle:zero .........................   Passed    0.07 sec
            Start 562: TestMliapPyUnified
    562/563 Test #562: TestMliapPyUnified .........................   Passed    0.16 sec
            Start 563: TestPairList
    563/563 Test #563: TestPairList ...............................   Passed    0.06 sec

    100% tests passed, 0 tests failed out of 563

    Label Time Summary:
    generated    =   0.85 sec*proc (3 tests)
    noWindows    =   4.16 sec*proc (2 tests)
    slow         =  78.33 sec*proc (67 tests)
    unstable     =  28.23 sec*proc (34 tests)

    Total Test time (real) = 132.34 sec

The `ctest` command has many options, the most important ones are:

Option | Function
`-V` | verbose output: display output of individual test runs
`-j <num>` | parallel run: run <num> tests in parallel
`-R <regex>` | run subset of tests matching the regular expression <regex>
`-E <regex>` | exclude subset of tests matching the regular expression <regex>
`-L <regex>` | run subset of tests with a label matching the regular expression <regex>
`-LE <regex>` | exclude subset of tests with a label matching the regular expression <regex>
`-N` | dry-run: display list of tests without running them
`-T memcheck` | run tests with valgrind memory checker (if available)

In its full implementation, the unit test framework will consist of multiple kinds of tests implemented in different programming languages (C++, C, Python, Fortran) and testing different aspects of the LAMMPS software and its features. The tests will adapt to the compilation settings of LAMMPS, so that tests will be skipped if prerequisite features are not available in LAMMPS.

Work in Progress

The unit test framework was added in spring 2020 and is under active development. The coverage is not complete and will be expanded over time. Preference is given to parts of the code base that are easy to test or commonly used.

Tests as shown by the `ctest` program are commands defined in the `CMakeLists.txt` files in the `unittest` directory tree. A few tests simply execute LAMMPS with specific command-line flags and check the output to the screen for expected content. A large number of unit tests are special tests programs using the GoogleTest framework and linked to the LAMMPS library that test individual functions or create a LAMMPS class instance, execute one or more commands and check data inside the LAMMPS class hierarchy. There are also tests for the C-library, Fortran, and Python module interfaces to LAMMPS. The Python tests use the Python “unittest” module in a similar fashion than the others use GoogleTest. These special test programs are structured to perform multiple individual tests internally and each of those contains several checks (aka assertions) for internal data being changed as expected.

Tests for force computing or modifying styles (e.g. styles for non-bonded and bonded interactions and selected fixes) are run by using a more generic test program that reads its input from files in YAML format. The YAML file provides the information on how to customized the test program to test a specific style and - if needed - with specific settings. To add a test for another, similar style (e.g. a new pair style) it is usually sufficient to add a suitable YAML file. Detailed instructions for adding tests are provided in the Programmer Guide part of the manual. A description of what happens during the tests is given below.

### Unit tests for force styles

A large part of LAMMPS are different “styles” for computing non-bonded and bonded interactions selected through the pair_style command, bond_style command, angle_style command, dihedral_style command, improper_style command, and kspace_style command. Since these all share common interfaces, it is possible to write generic test programs that will call those common interfaces for small test systems with less than 100 atoms and compare the results with pre-recorded reference results. A test run is then a a collection multiple individual test runs each with many comparisons to reference results based on template input files, individual command settings, relative error margins, and reference data stored in a YAML format file with `.yaml` suffix. Currently the programs `test_pair_style`, `test_bond_style`, `test_angle_style`, `test_dihedral_style`, and `test_improper_style` are implemented. They will compare forces, energies and (global) stress for all atoms after a `run 0` calculation and after a few steps of MD with fix nve, each in multiple variants with different settings and also for multiple accelerated styles. If a prerequisite style or package is missing, the individual tests are skipped. All force style tests will be executed on a single MPI process, so using the CMake option `-D BUILD_MPI=off` can significantly speed up testing, since this will skip the MPI initialization for each test run. Below is an example command and output:

    $ test_pair_style mol-pair-lj_cut.yaml
    [==========] Running 6 tests from 1 test suite.
    [----------] Global test environment set-up.
    [----------] 6 tests from PairStyle
    [ RUN      ] PairStyle.plain
    [       OK ] PairStyle.plain (24 ms)
    [ RUN      ] PairStyle.omp
    [       OK ] PairStyle.omp (18 ms)
    [ RUN      ] PairStyle.intel
    [       OK ] PairStyle.intel (6 ms)
    [ RUN      ] PairStyle.opt
    [  SKIPPED ] PairStyle.opt (0 ms)
    [ RUN      ] PairStyle.single
    [       OK ] PairStyle.single (7 ms)
    [ RUN      ] PairStyle.extract
    [       OK ] PairStyle.extract (6 ms)
    [----------] 6 tests from PairStyle (62 ms total)

    [----------] Global test environment tear-down
    [==========] 6 tests from 1 test suite ran. (63 ms total)
    [  PASSED  ] 5 tests.
    [  SKIPPED ] 1 test, listed below:
    [  SKIPPED ] PairStyle.opt

In this particular case, 5 out of 6 sets of tests were conducted, the tests for the `lj/cut/opt` pair style was skipped, since the tests executable did not include it. To learn what individual tests are performed, you (currently) need to read the source code. You can use code coverage recording (see next section) to confirm how well the tests cover the code paths in the individual source files.

The force style test programs have a common set of options:

Option | Function
`-g <newfile>` | regenerate reference data in new YAML file
`-u` | update reference data in the original YAML file
`-s` | print error statistics for each group of comparisons
`-v` | verbose output: also print the executed LAMMPS commands

The `ctest` tool has no mechanism to directly pass flags to the individual test programs, but a workaround has been implemented where these flags can be set in an environment variable `TEST_ARGS`. Example:

    env TEST_ARGS=-s ctest -V -R BondStyle

To add a test for a style that is not yet covered, it is usually best to copy a YAML file for a similar style to a new file, edit the details of the style (how to call it, how to set its coefficients) and then run test command with either the `-g` and the replace the initial test file with the regenerated one or the `-u` option. The `-u` option will destroy the original file, if the generation run does not complete, so using `-g` is recommended unless the YAML file is fully tested and working.

Some of the force style tests are rather slow to run and some are very sensitive to small differences like CPU architecture, compiler toolchain, compiler optimization. Those tests are flagged with a “slow” and/or “unstable” label, and thus those tests can be selectively excluded with the `-LE` flag or selected with the `-L` flag.

Recommendations and notes for YAML files

- The reference results should be recorded without any code optimization or related compiler flags enabled.

- The `epsilon` parameter defines the relative precision with which the reference results must be met. The test geometries often have high and low energy parts and thus a significant impact from floating-point math truncation errors is to be expected. Some functional forms and potentials are more noisy than others, so this parameter needs to be adjusted. Typically a value around 1.0e-13 can be used, but it may need to be as large as 1.0e-8 in some cases.

- The tests for pair styles from OPT, OPENMP and INTEL are performed with automatically rescaled epsilon to account for additional loss of precision from code optimizations and different summation orders.

- When compiling with (aggressive) compiler optimization, some tests are likely to fail. It is recommended to inspect the individual tests in detail to decide, whether the specific error for a specific property is acceptable (it often is), or this may be an indication of mis-compiled code (or an undesired large loss of precision due to significant reordering of operations and thus less error cancellation).

### Unit tests for timestepping related fixes

A substantial subset of fix styles are invoked regularly during MD timestepping and manipulate per-atom properties like positions, velocities, and forces. For those fix styles, testing can be done in a very similar fashion as for force fields and thus there is a test program test_fix_timestep that shares a lot of code, properties, and command-line flags with the force field style testers described in the previous section.

This tester will set up a small molecular system run with verlet run style for 4 MD steps, then write a binary restart and continue for another 4 MD steps. At this point coordinates and velocities are recorded and compared to reference data. Then the system is cleared, restarted and running the second 4 MD steps again and the data is compared to the same reference. That is followed by another restart after which per atom type masses are replaced with per-atom masses and the second 4 MD steps are repeated again and compared to the same reference. Also global scalar and vector data of the fix is recorded and compared. If the fix is a thermostat and thus the internal property `t_target` can be extracted, then this is compared to the reference data. The tests are repeated with the respa run style.

If the fix has a multi-threaded version in the OPENMP package, then the entire set of tests is repeated for that version as well.

For this to work, some additional conditions have to be met by the YAML format test inputs.

- The fix to be tested (and only this fix), should be listed in the `prerequisites:` section

- The fix to be tested must be specified in the `post_commands:` section with the fix-ID `test`. This section may contain other commands and other fixes (e.g. an instance of fix nve for testing a thermostat or force manipulation fix)

- For fixes that can tally contributions to the global virial, the line `fix_modify test virial yes` should be included in the `post_commands:` section of the test input.

- For thermostat fixes the target temperature should be ramped from an arbitrary value (e.g. 50K) to a pre-defined target temperature entered as `${t_target}`.

- For fixes that have thermostatting support included, but do not have it enabled in the input (e.g. fix rigid with default settings), the `post_commands:` section should contain the line `variable t_target delete` to disable the target temperature ramp check to avoid false positives.

### Use custom linker for faster link times when ENABLE_TESTING is active

When compiling LAMMPS with enabled tests, most test executables will need to be linked against the LAMMPS library. Since this can be a very large library with many C++ objects when many packages are enabled, link times can become very long on machines that use the GNU BFD linker (e.g. Linux systems). Alternatives like the `mold` linker, the `lld` linker of the LLVM project, or the `gold` linker available with GNU binutils can speed up this step substantially (in this order). CMake will by default test if any of the three can be enabled and use it when `ENABLE_TESTING` is active. It can also be selected manually through the `CMAKE_CUSTOM_LINKER` CMake variable. Allowed values are `mold`, `lld`, `gold`, `bfd`, or `default`. The `default` option will use the system default linker otherwise, the linker is chosen explicitly. This option is only available for the GNU or Clang C++ compilers.

### Tests for other components and utility functions

Additional tests that validate utility functions or specific components of LAMMPS are implemented as standalone executable which may, or may not require creating a suitable LAMMPS instance. These tests are more specific and do not require YAML format input files. To add a test, either an existing source file needs to be extended or a new file added, which in turn requires additions to the `CMakeLists.txt` file in the source folder.

### Collect and visualize code coverage metrics

You can also collect code coverage metrics while running LAMMPS or the tests by enabling code coverage support during the CMake configuration:

    -D ENABLE_COVERAGE=on  # enable coverage measurements (off by default)

This will instrument all object files to write information about which lines of code were accessed during execution in files next to the corresponding object files. These can be post-processed to visually show the degree of coverage and which code paths are accessed and which are not taken. When working on unit tests (see above), this can be extremely helpful to determine which parts of the code are not executed and thus what kind of tests are still missing. The coverage data is cumulative, i.e. new data is added with each new run.

Enabling code coverage will also add the following build targets to generate coverage reports after running the LAMMPS executable or the unit tests:

    make gen_coverage_html   # generate coverage report in HTML format
    make gen_coverage_xml    # generate coverage report in XML format
    make clean_coverage_html # delete folder with HTML format coverage report
    make reset_coverage      # delete all collected coverage data and HTML output

These reports require GCOVR to be installed. The easiest way to do this to install it via pip:

    python3 -m pip install gcovr

After post-processing with `gen_coverage_html` the results are in a folder `coverage_html` and can be viewed with a web browser. The images below illustrate how the data is presented.

Top of the overview page

Styles with good coverage

Top of individual source page

Source page with branches

## 3.12.5. Coding style utilities

To aid with enforcing some of the coding style conventions in LAMMPS some additional build targets have been added. These require Python 3.5 or later and will only work properly on Unix-like operating and file systems.

The following options are available.

    make check-whitespace    # search for files with whitespace issues
    make fix-whitespace      # correct whitespace issues in files
    make check-homepage      # search for files with old LAMMPS homepage URLs
    make fix-homepage        # correct LAMMPS homepage URLs in files
    make check-errordocs     # search for deprecated error docs in header files
    make fix-errordocs       # remove error docs in header files
    make check-permissions   # search for files with permissions issues
    make fix-permissions     # correct permissions issues in files
    make check-docs          # search for several issues in the manual
    make check-version       # list files with pending release version tags
    make check               # run all check targets from above

These should help to make source and documentation files conforming to some the coding style preferences of the LAMMPS developers.

## 3.12.6. Clang-format support

For the code in the `unittest` and `src` trees we are transitioning to use the clang-format tool to assist with having a consistent source code formatting style. The clang-format command bundled with Clang version 8.0 or later is required. The configuration is in files called `.clang-format` in the respective folders. Since the modifications from clang-format can be significant and - especially for “legacy style code” - they are not always improving readability, a large number of files currently have a `// clang-format off` at the top, which will disable the processing. As of fall 2021 all files have been either “protected” this way or are enabled for full or partial clang-format processing. Over time, the “protected” files will be refactored and updated so that clang-format may be applied to them as well.

It is recommended for all newly contributed files to use the clang-format processing while writing the code or do the coding style processing (including the scripts mentioned in the previous paragraph)

If clang-format is available, files can be updated individually with commands like the following:

    clang-format -i some_file.cpp

The following target are available for both, GNU make and CMake:

    make format-src       # apply clang-format to all files in src and the package folders
    make format-tests     # apply clang-format to all files in the unittest tree

## 3.12.7. GitHub command-line interface

GitHub has developed a command-line tool to interact with the GitHub website via a command called `gh`. This is extremely convenient when working with a Git repository hosted on GitHub (like LAMMPS). It is thus highly recommended to install it when doing LAMMPS development. To use `gh` you must be within a git checkout of a repository and you must obtain an authentication token to connect your checkout with a GitHub user. This is done with the command: `gh auth login` where you then have to follow the prompts. Here are some examples:

Command | Description
--- | ---
`gh pr list` | List currently open pull requests
`gh pr checks 404` | Shows the status of all checks for pull request #404
`gh pr view 404` | Shows the description and recent comments for pull request #404
`gh co 404` | Check out the branch from pull request #404; set up for pushing changes
`gh issue list` | List currently open issues
`gh issue view 430 --comments` | Shows the description and all comments for issue #430

The capabilities of the `gh` command are continually expanding, so for more details please see the documentation at https://cli.github.com/manual/ or use `gh --help` or `gh <command> --help` for embedded help.