Build system overview

The GROMACS build system uses CMake (version 3.9.6 or newer is required) to generate the actual build system for the build tool choosen by the user. See CMake documentation for general introduction to CMake and how to use it. This documentation focuses on how the GROMACS build system is organized and implemented, and what features it provides to developers (some of which may be of interest to advanced users).

Most developers use make or ninja as the underlying build system, so there can be parts of the build system that are specifically designed for command-line consumption with these tools, and may not work ideally with other environments, but basic building should be possible with all the environments supported by CMake.

Also, the build system and version control is designed for out-of-source builds. In-source builds mostly work (there are a few custom targets that do not), but no particular effort has been put to, e.g., having .gitignore files that exclude all the build outputs, or to have the clean target remove all possible build outputs.

Build types

Build types is a CMake concept that provides overall control of how the build tools are used on the given platform to produce executable code. These can be set in CMake in various ways, including on a command line such as cmake -DCMAKE_BUILD_TYPE=Debug. GROMACS supports the following standard CMake build types:

Release

Fully optimized code intended for use in production simulation. This is the default.

Debug

Compiled code intended for use with debugging tools, with low optimization levels and debug information for symbols.

RelWithDebInfo

As Release, but with debug information for symbol names, which can help debugging issues that only emerge in optimized code.

MinSizeRel

As Release, but optimized to minimize the size of the resulting executable. This is never a concern for GROMACS installations, so should not be used, but probably works.

Additionally, GROMACS provides the following build types for development and testing. Their implementations can be found in cmake/gmxBuildTypeXXX.cmake.

Reference

This build type compiles a version of GROMACS aimed solely at correctness. All parallelization and optimization possibilities are disabled. This build type is compiled with gcc 5 to generate the regression test reference values, against which all other GROMACS builds are tested.

RelWithAssert

As Release, but removes -DNDEBUG from compiler command lines, which makes all assertion statements active (and can have other safety-related side effects in GROMACS and code upon which it depends)

Profile

As Release, but adds -pg for use with profiling tools. This is not likely to be effective for profiling the performance of gmx mdrun, but can be useful for the tools.

TSAN

Builds GROMACS for use with ThreadSanitzer in gcc and clang (http://clang.llvm.org/docs/ThreadSanitizer.html) to detect data races. This disables the use of atomics in ThreadMPI, preferring the mutex-based implementation.

ASAN

Builds GROMACS for use with AddressSanitzer in gcc and clang (http://clang.llvm.org/docs/AddressSanitizer.html) to detect many kinds of memory mis-use. By default, AddressSanitizer includes LeakSanitizer.

MSAN

Builds GROMACS for use with AddressSanitzer in clang (http://clang.llvm.org/docs/MemorySanitizer.html) to detect reads of unitialized memory. This functionality requires that dependencies of the GROMACS build have been built in a compatible way (roughly, static libraries with -g -fsanitize=memory -fno-omit-frame-pointer), which generally requires at least the C++ standard library to have been built specially. The path where the includes and libraries for dependencies should be found for this build type is set in the CMake cache variable GMX_MSAN_PATH. Only internal XDR and internal fftpack are supported at this time.

For all of the sanitizer builds, to get readable stack traces, you may need to ensure that the ASAN_SYMBOLIZER_PATH environment variable (or your PATH) include that of the llvm-symbolizer binary.

With some generators, CMake generates the build system for more than a single CMAKE_BUILD_TYPE from one pass over the CMakeLists.txt files, so any code that uses CMAKE_BUILD_TYPE in CMakeLists.txt directly will break. GROMACS does use such CMake code, so we do not fully support all these build types in such generators (which includes Visual Studio).

CMake cache variables

This section provides a (currently incomplete) list of cache variables that developers or advanced users can set to affect what CMake generates and/or what will get built.

Compiler flags

Standard CMake mechanism for specifying the compiler flags is to use CMAKE_C_FLAGS/CMAKE_CXX_FLAGS for flags that affect all build types, and CMAKE_C_FLAGS_buildtype/CMAKE_CXX_FLAGS_buildtype for flags that only affect a specific build type. CMake provides some default flags.

GROMACS determines its own set of default flags, grouped into two categories:

• Generic flags that are appended to the above default CMake flag variables (possibly for multiple build types), generally specifying optimization flags to use and controlling compiler warnings.
• Specific flags for certain features that the build system determines to be necessary for successful compilation. One example is flags that determine what SIMD instruction set the compiler is allowed to use/needs to support.

All of the above flags are only added after testing that they work with the provided compiler.

There is one cache variable to control the behavior of automatic compiler flags:

GMX_SKIP_DEFAULT_CFLAGS

If set ON, the build system will not add any compiler flags automatically (neither generic nor specific as defined above), and will skip most linker flags as well. The default flags that would have been added are instead printed out when cmake is run, and the user can set the flags themselves using the CMake variables. If OFF (the default), the flags are added as described above.

The code the determine the default generic flags is in cmake/gmxCFlags.cmake. Code that sets the specific flags (e.g., SIMD flags) is in the main CMakeLists.txt; search for GMX_SKIP_DEFAULT_CFLAGS. The variables used there can be traced back to the locations where the actual flags to use are determined.

Variables affecting compilation/linking

GMX_BROKEN_CALLOC

GMX_BUILD_FOR_COVERAGE

Special variable set ON by Jenkins when doing a build for the coverage job. Allows the build system to set options to produce as useful coverage metrics as possible. Currently, it disables all asserts to avoid them showing up as poor conditional coverage. Defaults to OFF, and there should not be any need to change this in a manual build.

GMX_BUILD_MDRUN_ONLY

If set ON, the build system is configured to only build and install a single mdrun executable. To be fully functional, the installed mdrun requires a standard GROMACS installation (with GMX_BUILD_MDRUN_ONLY=OFF) in the same installation prefix, as the mdrun-only build does not install any data files or scripts, only the binary. This is intended for cases where one wants to/needs to compile one or more instances of mdrun with different build options (e.g., MPI or SIMD) than the full installation with the other utilities. Defaults to OFF, in which case a single gmx executable is built and installed, together with all the supporting files. mdrun can be executed as gmx mdrun.

GMX_BUILD_OWN_FFTW

GMX_BUILD_SHARED_EXE

GMX_COMPILER_WARNINGS

If set ON, various compiler warnings are enabled for compilers that Jenkins uses for verification. Defaults to OFF when building from a source tarball so that users compiling with versions not tested on Jenkins are not exposed to our rather aggressive warning flags that can trigger a lot of warnings with, e.g., new versions of the compilers we use. When building from a git repository, defaults to ON.

GMX_CYCLE_SUBCOUNTERS

If set to ON, enables performance subcounters that offer more fine-grained mdrun performance measurement and evaluation than the default counters. See Getting good performance from mdrun for the description of subcounters which are available. Defaults to OFF.

GMX_ENABLE_CCACHE

If set to ON, attempts to set up the ccache caching compiler wrapper to speed up repeated builds. The ccache executable is searched for with find_package() if CMake is being run with a compatible build type. If the executable is found and a compatible compiler is configured, CMake launch wrapper scripts are set. If enabled, the ccache executable location discovered by CMake must be accessible during build, as well. Defaults to OFF to minimize build system complexity.

GMX_INSTALL_DATASUBDIR

Sets the subdirectory under CMAKE_INSTALL_DATADIR where GROMACS-specific read-only architecture-independent data files are installed. The default is gromacs, which means the files will go under share/gromacs. To alter the share part, change CMAKE_INSTALL_DATADIR. See Relocatable binaries for how this influences the build.

GMX_DOUBLE

Many part of GROMACS are implemented in terms of “real” precision, which is actually either a single- or double-precision type, according to the value of this flag. Some parts of the code deliberately use single- or double-precision types, and these are unaffected by this setting. See reference manual for further information.

GMX_RELAXED_DOUBLE_PRECISION

Permit a double-precision configuration to compute some quantities to single-precision accuracy. Particularly on architectures where only double-precision SIMD is available (e.g. Sparc machines such as the K computer), it is faster to default to GMX_DOUBLE=ON and use SIMD than to use GMX_DOUBLE=OFF and use no SIMD. However, if the user does not need full double precision, then some optimizations can achieve the equivalent of single-precision results (e.g. fewer Newton-Raphson iterations for a reciprocal square root computation).

GMX_EXTRAE

GMX_EXTERNAL_BLAS

GMX_EXTERNAL_LAPACK

GMX_EXTERNAL_TNG

GMX_FFT_LIBRARY

GMX_GIT_VERSION_INFO

Whether to generate version information dynamically from git for each build (e.g., HEAD commit hash). Defaults to ON if the build is from a git repository and git is found, otherwise OFF. If OFF, static version information from cmake/gmxVersionInfo.cmake is used.

GMX_GPU

GMX_CLANG_CUDA

Use clang for compiling CUDA GPU code, both host and device.

GMX_CUDA_CLANG_FLAGS

Pass additional CUDA-only compiler flags to clang using this variable.

CMAKE_INSTALL_LIBDIR

Sets the installation directory for libraries (default is determined by standard CMake package GNUInstallDirs). See Relocatable binaries for how this influences the build.

GMX_LOAD_PLUGINS

GMX_MPI

GMX_OPENMP

GMX_PREFER_STATIC_LIBS

GMX_SIMD

GMX_SOFTWARE_INVSQRT

GMX_THREAD_MPI

GMX_USE_RDTSCP

GMX_USE_TNG

GMX_VMD_PLUGIN_PATH

GMX_X11

GMX_XML

Currently, this option has no effect on the compilation or linking, since there is no code outside the tests that would use libxml2.

Variables affecting the all target

BUILD_TESTING

Standard variable created by CTest that enables/disables all tests. Defaults to ON.

GMX_BUILD_HELP

Controls handling of man pages and shell completions. Possible values:

OFF (default for builds from release source distribution)

Man pages and shell completions are not generated as part of the all target, and only installed if compiling from a source package.

AUTO (default for builds from development version)

Shell completions are generated by executing the gmx binary as part of the all target. If it fails, a message is printed, but the build succeeds. Man pages need to be generated manually by invoking the man target. Man pages and shell completions are installed if they have been successfully generated.

ON

Works the same as AUTO, except that if invoking the gmx binary fails, the build fails as well.

GMX_DEVELOPER_BUILD

If set ON, the all target will include also the test binaries using Google Test (if GMX_BUILD_UNITTESTS is ON). Also, GMX_COMPILER_WARNINGS is always enabled. In the future, other developer convenience features (as well as features inconvenient for a general user) can be added to the set controlled by this variable.

GMX_CLANG_TIDY

clang-tidy is used for static code analysis and (some) automated fixing of issues detected. clang-tidy is easy to install. It is contained in the llvm binary package. Only version 8.0.* with libstdc++<7 or libc++ is supported. Others might miss tests or give false positives. It is run automatically on Jenkins for each commit. Many checks have fixes which can automatically be applied. To run it, the build has to be configured with cmake -DGMX_CLANG_TIDY=ON -DGMX_OPENMP=no -DCMAKE_BUILD_TYPE=Debug -DCMAKE_EXPORT_COMPILE_COMMANDS=on. Any CMAKE_BUILD_TYPE which enables asserts (e.g. ASAN) works. Such a configured build will run both the compiler as well as clang-tidy when building. The name of the clang-tidy executable is set with -DCLANG_TIDY=..., and the full path to it can be set with -DCLANG_TIDY_EXE=.... To apply the automatic fixes to the issue identified clang-tidy should be run seperately (running clang-tidy with -fix-errors as part of the build can corrupt header files). To fix a specific file run clang-tidy -fix-errors -header-filter '.*' {file}, to fix all files in parallel run-clang-tidy.py -fix -header-filter '.*' '(?<!/selection/parser\.cpp|selection/scanner\.cpp)$', and to fix all modified files run-clang-tidy.py -fix -header-filter '.*' $(git diff HEAD --name-only). The run-clang-tidy.py script is in the share/clang/ subfolder of the llvm distribution. clang-tidy has to be able to find the compile_commands.json file. Either run from the build folder or add a symlink to the source folder. GMX_ENABLE_CCACHE does not work with clang-tidy.

Variables affecting special targets

GMXAPI

If set ON, the additional gmxapi C++ library is configured and the gmxapi headers will be installed. Provides the additional build tree targets gmxapi-cppdocs and gmxapi-cppdocs-dev when Doxygen is available. Also exports CMake configuration files for gmxapi that allow find_package(gmxapi) to import the Gromacs::gmxapi CMake target in client projects that search the GROMACS installation root.

GMX_BUILD_MANUAL

If set ON, CMake detection for LaTeX and other prerequisites for the reference PDF manual is done, and the manual target for building the manual is generated. If OFF (the default), all detection is skipped and the manual cannot be built.

GMX_BUILD_TARBALL

If set ON, -dev suffix is stripped off from version strings and some other version info logic is adjusted such that the man pages and other documentation generated from this build is suitable for releasing (on the web page and/or in the source distribution package). Defaults to OFF.

GMX_BUILD_UNITTESTS

If ON, test binaries using Google Test are built (either as the separate tests targer, or also as part of the all target, depending on GMX_DEVELOPER_BUILD). All dependencies required for building the tests (Google Test and Google Mock frameworks, and tinyxml2) are included in src/external/. Defaults to ON if BUILD_TESTING is ON.

GMX_COMPACT_DOXYGEN

If set ON, Doxygen configuration is changed to avoid generating large dependency graphs, which makes it significantly faster to run Doxygen and reduces disk usage. This is typically useful when developing the documentation to reduce the build times. Defaults to OFF.

REGRESSIONTEST_DOWNLOAD

If set ON, CMake will download the regression tests and extract them to a local directory. REGRESSIONTEST_PATH is set to the extracted tests. Note that this happens during the configure phase, not during the build. After the download is done, the variable is automatically reset to OFF again to avoid repeated downloads. Can be set to ON to download again. Defaults to OFF.

REGRESSIONTEST_PATH

Path to extracted regression test suite matching the source tree (the directory containing gmxtest.pl) If set, CTest tests are generated to run the regression tests. Defaults to empty.

SOURCE_MD5SUM

Sets the MD5 sum of the release tarball when generating the HTML documentation. It gets inserted into the download section of the HTML pages.

External libraries

Special targets

In addition to the default all target, the generated build system has several custom targets that are intended to be explicitly built to perform various tasks (some of these may also run automatically). There are various other targets as well used internally by these, but those are typically not intended to be invoked directly.

check

Builds all the binaries needed by the tests and runs the tests. If some types of tests are not available, shows a note to the user. This is the main target intended for normal users to run the tests. See Unit testing.

check-source

Runs a custom Python checker script to check for various source-level issues. Uses Doxygen XML documentation as well as rudimentary parsing of some parts of the source files. This target is used as part of the Jenkins documentation job. All CMake code is currently in docs/doxygen/. See Source tree checker scripts.

completion

Runs the compiled gmx executable to generate shell command-line completion definitions. This target is only added if GMX_BUILD_HELP is not OFF, and it is run automatically as part of the default all target. See GMX_BUILD_HELP. All CMake code is in src/programs/.

dep-graphs*

Builds include dependency graphs for the source files using dot from graphviz. All CMake code is in docs/doxygen/. See Source tree checker scripts.

doxygen-*

Targets that run Doxygen to generate the documentation. The doxygen-all target runs as part of the webpage target, which in turn runs as part of the Jenkins documentation job. All CMake code is in docs/doxygen/. See Using Doxygen.

gmxapi-cppdocs

Builds API documentation for gmxapi. Useful to authors of client software. Documentation is generated in docs/api-user in the build directory.

gmxapi-cppdocs-dev

Extract documentation for gmxapi and GROMACS developers to docs/api-dev.

install-guide

Runs Sphinx to generate a plain-text INSTALL file for the source package. The files is generated at docs/install-guide/text/, from where it gets put at the root of the source package by CPack. All CMake code is in docs/.

man

Runs Sphinx to generate man pages for the programs. Internally, also runs the compiled gmx executable to generate the input files for Sphinx. All CMake code is in docs/. See GMX_BUILD_HELP for information on when the man pages are installed.

manual

Runs LaTeX to generate the reference PDF manual. All CMake code is in docs/manual/. See GMX_BUILD_MANUAL.

package_source

Standard target created by CPack that builds a source package. This target is used to generate the released source packages.

test

Standard target created by CTest that runs all the registered tests. Note that this does not build the test binaries, only runs them, so you need to first ensure that they are up-to-date. See Unit testing.

tests

Builds all the binaries needed by the tests (but not gmx). See Unit testing.

webpage

Collection target that runs the other documentation targets to generate the full set of HTML (and linked) documentaion. This target is used as part of the Jenkins documentation job. All CMake code is in docs/.

webpage-sphinx

Runs Sphinx to generate most content for the HTML documentation (the set of web pages this developer guide is also part of). Internally, also runs the compiled gmx executable to generate some input files for Sphinx. All CMake code is in docs/.

Passing information to source code

The build system uses a few different mechanisms to influence the compilation:

• On the highest level, some CMake options select what files will be compiled.

• Some options are passed on the compiler command line using -D or equivalent, such that they are available in every compilation unit. This should be used with care to keep the compiler command lines manageable. You can find the current set of such defines with

  git grep add_definitions
  

• A few header files are generated using CMake configure_file() and included in the desired source files. These files must exist for the compilation to pass. Only a few files use an #ifdef HAVE_CONFIG_H to protect against inclusion in case the define is not set; this is used in files that may get compiled outside the main build system.

  buildinfo.h

  Contains various strings about the build environment, used mainly for outputting version information to log files and when requested.

  config.h

  Contains defines for conditional compilation within source files.

  gmxpre-config.h

  Included by gmxpre.h as the first thing in every source file. Should only contain defines that are required before any other header for correct operation. For example, defines that affect the behavior of system headers fall in this category. See Doxygen documentation for gmxpre.h.

  All the above files get generated in src/.

  Additionally, the following file is generated by the build system:

  baseversion-gen.cpp

  Provides definitions for declarations in baseversion_gen.h for version info output. The contents are generated either from Git version info, or from static version info if not building from a git repository.