6 The |Gromacs| build system uses CMake (version
7 |CMAKE_MINIMUM_REQUIRED_VERSION| or newer is required) to generate the
8 actual build system for the build tool choosen by the user. See CMake
9 documentation for general introduction to CMake and how to use it. This
10 documentation focuses on how the |Gromacs| build system is organized and
11 implemented, and what features it provides to developers (some of which may be
12 of interest to advanced users).
14 Most developers use ``make`` or ``ninja`` as the underlying build system, so
15 there can be parts of the build system that are specifically designed for
16 command-line consumption with these tools, and may not work ideally with other
17 environments, but basic building should be possible with all the environments
20 Also, the build system and version control is designed for out-of-source
21 builds. In-source builds mostly work (there are a few custom targets that do
22 not), but no particular effort has been put to, e.g., having :file:`.gitignore`
23 files that exclude all the build outputs, or to have the ``clean`` target
24 remove all possible build outputs.
29 Build types is a CMake concept that provides overall control of how
30 the build tools are used on the given platform to produce executable
31 code. These can be set in CMake in various ways, including on a
32 command line such as ``cmake -DCMAKE_BUILD_TYPE=Debug``. |Gromacs|
33 supports the following standard CMake build types:
36 Fully optimized code intended for use in production simulation. This is the
40 Compiled code intended for use with debugging tools, with low optimization levels
41 and debug information for symbols.
44 As Release, but with debug information for symbol names, which can help debugging
45 issues that only emerge in optimized code.
48 As Release, but optimized to minimize the size of the resulting executable. This
49 is never a concern for |Gromacs| installations, so should not be used, but
52 Additionally, |Gromacs| provides the following build types for development and
53 testing. Their implementations can be found in ``cmake/gmxBuildTypeXXX.cmake``.
56 This build type compiles a version of |Gromacs| aimed solely at correctness. All
57 parallelization and optimization possibilities are disabled. This build type is
58 compiled with gcc 5 to generate the regression test reference values, against
59 which all other |Gromacs| builds are tested.
62 As Release, but removes ``-DNDEBUG`` from compiler command lines, which makes
63 all assertion statements active (and can have other safety-related side effects
64 in |Gromacs| and code upon which it depends)
67 As Release, but adds ``-pg`` for use with profiling tools. This is not
68 likely to be effective for profiling the performance of :ref:`gmx mdrun`, but can
69 be useful for the tools.
72 Builds |Gromacs| for use with ThreadSanitzer in gcc and clang
73 (http://clang.llvm.org/docs/ThreadSanitizer.html) to detect
74 data races. This disables the use of atomics in ThreadMPI,
75 preferring the mutex-based implementation.
78 Builds |Gromacs| for use with AddressSanitzer in gcc and
79 clang (http://clang.llvm.org/docs/AddressSanitizer.html) to
80 detect many kinds of memory mis-use. By default, AddressSanitizer
81 includes LeakSanitizer.
84 Builds |Gromacs| for use with AddressSanitzer in clang
85 (http://clang.llvm.org/docs/MemorySanitizer.html) to detect
86 reads of unitialized memory. This functionality requires that
87 dependencies of the |Gromacs| build have been built in a compatible
88 way (roughly, static libraries with ``-g -fsanitize=memory
89 -fno-omit-frame-pointer``), which generally requires at least the C++
90 standard library to have been built specially. The path where the
91 includes and libraries for dependencies should be found for this
92 build type is set in the CMake cache variable
93 ``GMX_MSAN_PATH``. Only internal XDR and internal fftpack are
94 supported at this time.
96 For all of the sanitizer builds, to get readable stack traces, you may
97 need to ensure that the ``ASAN_SYMBOLIZER_PATH`` environment variable
98 (or your ``PATH``) include that of the ``llvm-symbolizer`` binary.
100 With some generators, CMake generates the build system for more than a
101 single ``CMAKE_BUILD_TYPE`` from one pass over the ``CMakeLists.txt``
102 files, so any code that uses ``CMAKE_BUILD_TYPE`` in
103 ``CMakeLists.txt`` directly will break. |Gromacs| does use such CMake
104 code, so we do not fully support all these build types in such
105 generators (which includes Visual Studio).
107 CMake cache variables
108 ---------------------
110 This section provides a (currently incomplete) list of cache variables that
111 developers or advanced users can set to affect what CMake generates and/or what
116 Figure out where to document basic variables intended for user
117 consumption, and how does it relate to documentation here.
121 Document the remaining variables below, and identify any variables
122 missing from the list.
127 Standard CMake mechanism for specifying the compiler flags is to use
128 ``CMAKE_C_FLAGS``/``CMAKE_CXX_FLAGS`` for flags that affect all build types,
129 and :samp:`CMAKE_C_FLAGS_{buildtype}`/:samp:`CMAKE_CXX_FLAGS_{buildtype}` for
130 flags that only affect a specific build type. CMake provides some default flags.
132 |Gromacs| determines its own set of default flags, grouped into two categories:
134 * Generic flags that are appended to the above default CMake flag variables
135 (possibly for multiple build types), generally specifying optimization flags
136 to use and controlling compiler warnings.
137 * Specific flags for certain features that the build system determines to be
138 necessary for successful compilation. One example is flags that determine
139 what SIMD instruction set the compiler is allowed to use/needs to support.
141 All of the above flags are only added after testing that they work with the
144 There is one cache variable to control the behavior of automatic compiler flags:
146 .. cmake:: GMX_SKIP_DEFAULT_CFLAGS
148 If set ``ON``, the build system will not add any compiler flags
149 automatically (neither generic nor specific as defined above), and will skip
150 most linker flags as well.
151 The default flags that would have been added are instead printed out when
152 :command:`cmake` is run, and the user can set the flags themselves using the
154 If ``OFF`` (the default), the flags are added as described above.
156 The code the determine the default generic flags is in
157 :file:`cmake/gmxCFlags.cmake`.
158 Code that sets the specific flags (e.g., SIMD flags) is in the main
159 :file:`CMakeLists.txt`; search for :cmake:`GMX_SKIP_DEFAULT_CFLAGS`.
160 The variables used there can be traced back to the locations where the actual
161 flags to use are determined.
163 Variables affecting compilation/linking
164 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
166 .. cmake:: GMX_BROKEN_CALLOC
168 .. cmake:: GMX_BUILD_FOR_COVERAGE
170 Special variable set ``ON`` by Jenkins when doing a build for the coverage
171 job. Allows the build system to set options to produce as useful coverage
172 metrics as possible. Currently, it disables all asserts to avoid them
173 showing up as poor conditional coverage.
174 Defaults to ``OFF``, and there should not be any need to change this in a
177 .. todo:: This could likely be replaced by a (yet another) build type.
179 .. cmake:: GMX_BUILD_OWN_FFTW
181 .. cmake:: GMX_BUILD_SHARED_EXE
183 .. cmake:: GMX_COMPILER_WARNINGS
185 If set ``ON``, various compiler warnings are enabled for compilers that
186 Jenkins uses for verification.
187 Defaults to ``OFF`` when building from a source tarball so that users
188 compiling with versions not tested on Jenkins are not exposed to our rather
189 aggressive warning flags that can trigger a lot of warnings with, e.g., new
190 versions of the compilers we use.
191 When building from a git repository, defaults to ``ON``.
193 .. cmake:: GMX_CYCLE_SUBCOUNTERS
195 If set to ``ON``, enables performance subcounters that offer more
196 fine-grained mdrun performance measurement and evaluation than the default
197 counters. See :doc:`/user-guide/mdrun-performance` for the description of
198 subcounters which are available.
201 .. cmake:: GMX_ENABLE_CCACHE
203 If set to ``ON``, attempts to set up the `ccache <https://ccache.samba.org>`_
204 caching compiler wrapper to speed up repeated builds.
205 The ``ccache`` executable is searched for with ``find_package()`` if CMake
206 is being run with a compatible build type.
207 If the executable is found and a compatible compiler is configured,
208 CMake launch wrapper scripts are set.
209 If enabled, the ``ccache`` executable location discovered by CMake must be
210 accessible during build, as well.
211 Defaults to ``OFF`` to minimize build system complexity.
213 .. cmake:: GMX_INSTALL_DATASUBDIR
215 Sets the subdirectory under CMAKE_INSTALL_DATADIR where GROMACS-specific
216 read-only architecture-independent data files are installed. The default
217 is ``gromacs``, which means the files will go under ``share/gromacs``.
218 To alter the ``share`` part, change CMAKE_INSTALL_DATADIR.
219 See :doc:`relocatable-binaries` for how this influences the build.
221 .. cmake:: GMX_DOUBLE
223 Many part of |Gromacs| are implemented in terms of "real" precision,
224 which is actually either a single- or double-precision type,
225 according to the value of this flag. Some parts of the code
226 deliberately use single- or double-precision types, and these are
227 unaffected by this setting. See reference manual for further
230 .. cmake:: GMX_EXTRAE
232 .. cmake:: GMX_EXTERNAL_BLAS
234 .. cmake:: GMX_EXTERNAL_LAPACK
236 .. cmake:: GMX_EXTERNAL_TNG
238 .. cmake:: GMX_FFT_LIBRARY
240 .. cmake:: GMX_GIT_VERSION_INFO
242 Whether to generate version information dynamically from git for each build
243 (e.g., HEAD commit hash).
244 Defaults to ``ON`` if the build is from a git repository and :command:`git`
245 is found, otherwise ``OFF``.
246 If ``OFF``, static version information from
247 :file:`cmake/gmxVersionInfo.cmake` is used.
251 .. cmake:: GMX_CLANG_CUDA
253 Use clang for compiling CUDA GPU code, both host and device.
255 .. cmake:: GMX_CUDA_CLANG_FLAGS
257 Pass additional CUDA-only compiler flags to clang using this variable.
259 .. cmake:: CMAKE_INSTALL_LIBDIR
261 Sets the installation directory for libraries (default is determined by
262 standard CMake package ``GNUInstallDirs``).
263 See :doc:`relocatable-binaries` for how this influences the build.
265 .. cmake:: GMX_LOAD_PLUGINS
269 .. cmake:: GMX_OPENMP
271 .. cmake:: GMX_PREFER_STATIC_LIBS
275 .. cmake:: GMX_SOFTWARE_INVSQRT
277 .. cmake:: GMX_THREAD_MPI
279 .. cmake:: GMX_USE_RDTSCP
281 .. cmake:: GMX_USE_TNG
283 .. cmake:: GMX_VMD_PLUGIN_PATH
289 Currently, this option has no effect on the compilation or linking, since
290 there is no code outside the tests that would use :file:`libxml2`.
292 Variables affecting the ``all`` target
293 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
295 .. cmake:: BUILD_TESTING
297 Standard variable created by CTest that enables/disables all tests.
300 .. cmake:: GMX_BUILD_HELP
302 Controls handling of man pages and shell completions. Possible values:
304 ``OFF`` (default for builds from release source distribution)
305 Man pages and shell completions are not generated as part of the ``all``
306 target, and only installed if compiling from a source package.
307 ``AUTO`` (default for builds from development version)
308 Shell completions are generated by executing the :file:`gmx` binary as
309 part of the ``all`` target. If it fails, a message is printed, but the
311 Man pages need to be generated manually by invoking the ``man`` target.
312 Man pages and shell completions are installed if they have been
313 successfully generated.
315 Works the same as ``AUTO``, except that if invoking the :file:`gmx` binary
316 fails, the build fails as well.
318 .. cmake:: GMX_DEVELOPER_BUILD
320 If set ``ON``, the ``all`` target will include also the test binaries using
321 Google Test (if :cmake:`GMX_BUILD_UNITTESTS` is ``ON``).
322 Also, :cmake:`GMX_COMPILER_WARNINGS` is always enabled.
323 In the future, other developer convenience features (as well as features
324 inconvenient for a general user) can be added to the set controlled by this
327 .. cmake:: GMX_CLANG_TIDY
329 `clang-tidy <http://releases.llvm.org/9.0.0/tools/clang/tools/extra/docs/clang-tidy/index.html>`_
330 is used for static code analysis and (some) automated fixing of issues detected. clang-tidy is easy to install. It is contained in
331 the llvm binary `package <http://releases.llvm.org/download.html#9.0.0>`_. Only
332 version 9.0.* with libstdc++<7 or libc++ is supported. Others might miss tests or give false positives.
333 It is run automatically in gitlab CI for each commit. Many checks have fixes which can automatically be
334 applied. To run it, the build has to be configured with
335 ``cmake -DGMX_CLANG_TIDY=ON -DCMAKE_BUILD_TYPE=Debug``.
336 Any ``CMAKE_BUILD_TYPE`` which enables asserts (e.g. ASAN) works. Such a configured build will
337 run both the compiler as well as clang-tidy when building. The name of the clang-tidy executable is set with
338 ``-DCLANG_TIDY=...``, and the full path to it can be set with ``-DCLANG_TIDY_EXE=...``.
339 To apply the automatic fixes to the issue identified clang-tidy should be run separately (running clang-tidy
340 with ``-fix-errors`` as part of the build can corrupt header files). To fix a specific file run
341 ``clang-tidy -fix-errors -header-filter '.*' {file}``, to fix all files in parallel
342 ``run-clang-tidy.py -fix -header-filter '.*' '(?<!/selection/parser\.cpp|selection/scanner\.cpp)$'``,
343 and to fix all modified files ``run-clang-tidy.py -fix -header-filter '.*' $(git diff HEAD --name-only)``.
344 The run-clang-tidy.py script is in the
345 ``share/clang/`` subfolder of the llvm distribution. ``clang-tidy`` has to be able to find the
346 ``compile_commands.json`` file. Either run from the build folder or add a symlink to the source folder.
347 :cmake:`GMX_ENABLE_CCACHE` does not work with clang-tidy.
349 Variables affecting special targets
350 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
354 If set ``ON``, the additional ``gmxapi`` C++ library is configured and the
355 ``gmxapi`` headers will be installed. Provides the additional build tree
356 targets ``gmxapi-cppdocs`` and ``gmxapi-cppdocs-dev`` when Doxygen is
357 available. Also exports CMake configuration files for ``gmxapi`` that allow
358 ``find_package(gmxapi)`` to import the ``Gromacs::gmxapi`` CMake target in
359 client projects that search the GROMACS installation root.
361 .. cmake:: GMX_BUILD_MANUAL
363 If set ``ON``, CMake detection for LaTeX and other prerequisites for the
364 reference PDF manual is done, and the ``manual`` target for building the
366 If ``OFF`` (the default), all detection is skipped and the manual cannot be
369 .. todo:: Consider if this is really necessary, or if we could just use
372 .. cmake:: GMX_BUILD_TARBALL
374 If set ``ON``, ``-dev`` suffix is stripped off from version strings and some
375 other version info logic is adjusted such that the man pages and other
376 documentation generated from this build is suitable for releasing (on the
377 web page and/or in the source distribution package).
380 .. cmake:: GMX_BUILD_UNITTESTS
382 If ``ON``, test binaries using Google Test are built (either as the separate
383 ``tests`` targer, or also as part of the ``all`` target, depending on
384 :cmake:`GMX_DEVELOPER_BUILD`). All dependencies required for building the
385 tests (Google Test and Google Mock frameworks, and tinyxml2) are
386 included in :file:`src/external/`.
387 Defaults to ``ON`` if :cmake:`BUILD_TESTING` is ``ON``.
389 .. cmake:: GMX_COMPACT_DOXYGEN
391 If set ``ON``, Doxygen configuration is changed to avoid generating large
392 dependency graphs, which makes it significantly faster to run Doxygen and
393 reduces disk usage. This is typically useful when developing the
394 documentation to reduce the build times.
397 .. cmake:: REGRESSIONTEST_DOWNLOAD
399 If set ``ON``, CMake will download the regression tests and extract them to
400 a local directory. :cmake:`REGRESSIONTEST_PATH` is set to the extracted
401 tests. Note that this happens during the configure phase, not during the
403 After the download is done, the variable is automatically reset to ``OFF``
404 again to avoid repeated downloads. Can be set to ``ON`` to download again.
407 .. cmake:: REGRESSIONTEST_PATH
409 Path to extracted regression test suite matching the source tree (the
410 directory containing :file:`gmxtest.pl`)
411 If set, CTest tests are generated to run the regression tests.
414 .. cmake:: SOURCE_MD5SUM
416 Sets the MD5 sum of the release tarball when generating the HTML
417 documentation. It gets inserted into the download section of the HTML
425 List external libraries used (either from src/external/, or from the
426 system), whether they are required or optional, what functionality they
427 provide for Gromacs, and how to control their use.
432 In addition to the default ``all`` target, the generated build system has
433 several custom targets that are intended to be explicitly built to perform
434 various tasks (some of these may also run automatically). There are various
435 other targets as well used internally by these, but those are typically not
436 intended to be invoked directly.
439 Builds all the binaries needed by the tests and runs the tests. If some
440 types of tests are not available, shows a note to the user.
441 This is the main target intended for normal users to run the tests.
442 See :doc:`testutils`.
444 Runs a custom Python checker script to check for various source-level
445 issues. Uses Doxygen XML documentation as well as rudimentary parsing of
446 some parts of the source files.
447 This target is used as part of the Jenkins documentation job.
448 All CMake code is currently in :file:`docs/doxygen/`.
451 Runs the compiled :file:`gmx` executable to generate shell command-line
452 completion definitions. This target is only added if
453 :cmake:`GMX_BUILD_HELP` is not ``OFF``, and it is run automatically as part
454 of the default ``all`` target. See :cmake:`GMX_BUILD_HELP`.
455 All CMake code is in :file:`src/programs/`.
457 Builds include dependency graphs for the source files using :command:`dot`
459 All CMake code is in :file:`docs/doxygen/`.
462 Targets that run Doxygen to generate the documentation.
463 The ``doxygen-all`` target runs as part of the ``webpage`` target, which in
464 turn runs as part of the Jenkins documentation job.
465 All CMake code is in :file:`docs/doxygen/`.
468 Builds API documentation for gmxapi. Useful to authors of client software.
469 Documentation is generated in :file:`docs/api-user` in the build directory.
471 Extract documentation for gmxapi and GROMACS developers to
472 :file:`docs/api-dev`.
474 Runs Sphinx to generate a plain-text INSTALL file for the source package.
475 The files is generated at :file:`docs/install-guide/text/`, from where it
476 gets put at the root of the source package by CPack.
477 All CMake code is in :file:`docs/`.
479 Runs Sphinx to generate man pages for the programs.
480 Internally, also runs the compiled :file:`gmx` executable to generate the
481 input files for Sphinx.
482 All CMake code is in :file:`docs/`.
483 See :cmake:`GMX_BUILD_HELP` for information on when the man pages are
486 Runs LaTeX to generate the reference PDF manual.
487 All CMake code is in :file:`docs/manual/`.
488 See :cmake:`GMX_BUILD_MANUAL`.
490 Standard target created by CPack that builds a source package.
491 This target is used to generate the released source packages.
493 Standard target created by CTest that runs all the registered tests.
494 Note that this does not build the test binaries, only runs them, so you need
495 to first ensure that they are up-to-date.
496 See :doc:`testutils`.
498 Builds all the binaries needed by the tests (but not ``gmx``).
499 See :doc:`testutils`.
501 Collection target that runs the other documentation targets to generate the
502 full set of HTML (and linked) documentaion.
503 This target is used as part of the Jenkins documentation job.
504 All CMake code is in :file:`docs/`.
506 Runs Sphinx to generate most content for the HTML documentation (the set of
507 web pages this developer guide is also part of).
508 Internally, also runs the compiled :file:`gmx` executable to generate some
509 input files for Sphinx.
510 All CMake code is in :file:`docs/`.
512 Passing information to source code
513 ----------------------------------
515 The build system uses a few different mechanisms to influence the compilation:
517 * On the highest level, some CMake options select what files will be compiled.
518 * Some options are passed on the compiler command line using ``-D`` or
519 equivalent, such that they are available in every compilation unit. This
520 should be used with care to keep the compiler command lines manageable.
521 You can find the current set of such defines with ::
523 git grep add_definitions
525 * A few header files are generated using CMake ``configure_file()`` and
526 included in the desired source files. These files must exist for the
527 compilation to pass. Only a few files use an ``#ifdef HAVE_CONFIG_H`` to
528 protect against inclusion in case the define is not set; this is used in
529 files that may get compiled outside the main build system.
532 Contains various strings about the build environment, used mainly for
533 outputting version information to log files and when requested.
535 Contains defines for conditional compilation within source files.
536 :file:`gmxpre-config.h`
537 Included by :file:`gmxpre.h` as the first thing in every source file.
538 Should only contain defines that are required before any other header for
539 correct operation. For example, defines that affect the behavior of system
540 headers fall in this category. See Doxygen documentation for
543 The above files are available through the INTERFACE_INCLUDE_DIR of
544 the ``common`` CMake target. I.e. to ``#include "config.h"``, be sure to
545 ``target_link_libraries(mymodule PRIVATE common)``
547 Additionally, the following file is generated by the build system:
549 :file:`baseversion-gen.cpp`
550 Provides definitions for declarations in :file:`baseversion_gen.h` for
551 version info output. The contents are generated either from Git version
552 info, or from static version info if not building from a git repository.