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
114 .. TODO: Figure out where to document basic variables intended for user
115 consumption, and how does it relate to documentation here.
117 .. TODO: Document the remaining variables below, and identify any variables
118 missing from the list.
123 Standard CMake mechanism for specifying the compiler flags is to use
124 ``CMAKE_C_FLAGS``/``CMAKE_CXX_FLAGS`` for flags that affect all build types,
125 and :samp:`CMAKE_C_FLAGS_{buildtype}`/:samp:`CMAKE_CXX_FLAGS_{buildtype}` for
126 flags that only affect a specific build type. CMake provides some default flags.
128 |Gromacs| determines its own set of default flags, grouped into two categories:
130 * Generic flags that are appended to the above default CMake flag variables
131 (possibly for multiple build types), generally specifying optimization flags
132 to use and controlling compiler warnings.
133 * Specific flags for certain features that the build system determines to be
134 necessary for successful compilation. One example is flags that determine
135 what SIMD instruction set the compiler is allowed to use/needs to support.
137 All of the above flags are only added after testing that they work with the
140 There is one cache variable to control the behavior of automatic compiler flags:
142 .. cmake:: GMX_SKIP_DEFAULT_CFLAGS
144 If set ``ON``, the build system will not add any compiler flags
145 automatically (neither generic nor specific as defined above), and will skip
146 most linker flags as well.
147 The default flags that would have been added are instead printed out when
148 :command:`cmake` is run, and the user can set the flags themselves using the
150 If ``OFF`` (the default), the flags are added as described above.
152 The code the determine the default generic flags is in
153 :file:`cmake/gmxCFlags.cmake`.
154 Code that sets the specific flags (e.g., SIMD flags) is in the main
155 :file:`CMakeLists.txt`; search for :cmake:`GMX_SKIP_DEFAULT_CFLAGS`.
156 The variables used there can be traced back to the locations where the actual
157 flags to use are determined.
159 Variables affecting compilation/linking
160 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
162 .. cmake:: GMX_BROKEN_CALLOC
164 .. cmake:: GMX_BUILD_FOR_COVERAGE
166 Special variable set ``ON`` by Jenkins when doing a build for the coverage
167 job. Allows the build system to set options to produce as useful coverage
168 metrics as possible. Currently, it disables all asserts to avoid them
169 showing up as poor conditional coverage.
170 Defaults to ``OFF``, and there should not be any need to change this in a
173 .. TODO: This could likely be replaced by a (yet another) build type.
175 .. cmake:: GMX_BUILD_MDRUN_ONLY
177 If set ``ON``, the build system is configured to only build and install a
178 single :file:`mdrun` executable. To be fully functional, the installed
179 :file:`mdrun` requires a standard |Gromacs| installation (with
180 ``GMX_BUILD_MDRUN_ONLY=OFF``) in the same installation prefix, as the
181 mdrun-only build does not install any data files or scripts, only the
182 binary. This is intended for cases where one wants to/needs to compile one
183 or more instances of :file:`mdrun` with different build options (e.g., MPI
184 or SIMD) than the full installation with the other utilities.
185 Defaults to ``OFF``, in which case a single :file:`gmx` executable is built
186 and installed, together with all the supporting files. :command:`mdrun` can
187 be executed as :command:`gmx mdrun`.
189 .. cmake:: GMX_BUILD_OWN_FFTW
191 .. cmake:: GMX_BUILD_SHARED_EXE
193 .. cmake:: GMX_COMPILER_WARNINGS
195 If set ``ON``, various compiler warnings are enabled for compilers that
196 Jenkins uses for verification.
197 Defaults to ``OFF`` when building from a source tarball so that users
198 compiling with versions not tested on Jenkins are not exposed to our rather
199 aggressive warning flags that can trigger a lot of warnings with, e.g., new
200 versions of the compilers we use.
201 When building from a git repository, defaults to ``ON``.
203 .. cmake:: GMX_CYCLE_SUBCOUNTERS
205 If set to ``ON``, enables performance subcounters that offer more
206 fine-grained mdrun performance measurement and evaluation than the default
207 counters. See :doc:`/user-guide/mdrun-performance` for the description of
208 subcounters which are available.
211 .. cmake:: GMX_ENABLE_CCACHE
213 If set to ``ON``, attempts to set up the `ccache <https://ccache.samba.org>`_
214 caching compiler wrapper to speed up repeated builds.
215 The ``ccache`` executable is searched for with ``find_package()`` if CMake
216 is being run with a compatible build type.
217 If the executable is found and a compatible compiler is configured,
218 CMake launch wrapper scripts are set.
219 If enabled, the ``ccache`` executable location discovered by CMake must be
220 accessible during build, as well.
221 Defaults to ``OFF`` to minimize build system complexity.
223 .. cmake:: GMX_INSTALL_DATASUBDIR
225 Sets the subdirectory under CMAKE_INSTALL_DATADIR where GROMACS-specific
226 read-only architecture-independent data files are installed. The default
227 is ``gromacs``, which means the files will go under ``share/gromacs``.
228 To alter the ``share`` part, change CMAKE_INSTALL_DATADIR.
229 See :doc:`relocatable-binaries` for how this influences the build.
231 .. cmake:: GMX_DOUBLE
233 Many part of |Gromacs| are implemented in terms of "real" precision,
234 which is actually either a single- or double-precision type,
235 according to the value of this flag. Some parts of the code
236 deliberately use single- or double-precision types, and these are
237 unaffected by this setting. See reference manual for further
240 .. cmake:: GMX_RELAXED_DOUBLE_PRECISION
242 Permit a double-precision configuration to compute some quantities
243 to single-precision accuracy. Particularly on architectures where
244 only double-precision SIMD is available (e.g. Sparc machines such
245 as the K computer), it is faster to default to ``GMX_DOUBLE=ON``
246 and use SIMD than to use ``GMX_DOUBLE=OFF`` and use no
247 SIMD. However, if the user does not need full double precision,
248 then some optimizations can achieve the equivalent of
249 single-precision results (e.g. fewer Newton-Raphson iterations for
250 a reciprocal square root computation).
252 .. cmake:: GMX_EXTRAE
254 .. cmake:: GMX_EXTERNAL_BLAS
256 .. cmake:: GMX_EXTERNAL_LAPACK
258 .. cmake:: GMX_EXTERNAL_TNG
260 .. cmake:: GMX_FFT_LIBRARY
262 .. cmake:: GMX_GIT_VERSION_INFO
264 Whether to generate version information dynamically from git for each build
265 (e.g., HEAD commit hash).
266 Defaults to ``ON`` if the build is from a git repository and :command:`git`
267 is found, otherwise ``OFF``.
268 If ``OFF``, static version information from
269 :file:`cmake/gmxVersionInfo.cmake` is used.
273 .. cmake:: GMX_CLANG_CUDA
275 Use clang for compiling CUDA GPU code, both host and device.
277 .. cmake:: GMX_CUDA_CLANG_FLAGS
279 Pass additional CUDA-only compiler flags to clang using this variable.
281 .. cmake:: CMAKE_INSTALL_LIBDIR
283 Sets the installation directory for libraries (default is determined by
284 standard CMake package ``GNUInstallDirs``).
285 See :doc:`relocatable-binaries` for how this influences the build.
287 .. cmake:: GMX_LOAD_PLUGINS
291 .. cmake:: GMX_OPENMP
293 .. cmake:: GMX_PREFER_STATIC_LIBS
297 .. cmake:: GMX_SOFTWARE_INVSQRT
299 .. cmake:: GMX_THREAD_MPI
301 .. cmake:: GMX_USE_RDTSCP
303 .. cmake:: GMX_USE_TNG
305 .. cmake:: GMX_VMD_PLUGIN_PATH
311 Currently, this option has no effect on the compilation or linking, since
312 there is no code outside the tests that would use :file:`libxml2`.
314 Variables affecting the ``all`` target
315 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
317 .. cmake:: BUILD_TESTING
319 Standard variable created by CTest that enables/disables all tests.
322 .. cmake:: GMX_BUILD_HELP
324 Controls handling of man pages and shell completions. Possible values:
326 ``OFF`` (default for builds from release source distribution)
327 Man pages and shell completions are not generated as part of the ``all``
328 target, and only installed if compiling from a source package.
329 ``AUTO`` (default for builds from development version)
330 Shell completions are generated by executing the :file:`gmx` binary as
331 part of the ``all`` target. If it fails, a message is printed, but the
333 Man pages need to be generated manually by invoking the ``man`` target.
334 Man pages and shell completions are installed if they have been
335 successfully generated.
337 Works the same as ``AUTO``, except that if invoking the :file:`gmx` binary
338 fails, the build fails as well.
340 .. cmake:: GMX_DEVELOPER_BUILD
342 If set ``ON``, the ``all`` target will include also the test binaries using
343 Google Test (if :cmake:`GMX_BUILD_UNITTESTS` is ``ON``).
344 Also, :cmake:`GMX_COMPILER_WARNINGS` is always enabled.
345 In the future, other developer convenience features (as well as features
346 inconvenient for a general user) can be added to the set controlled by this
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
423 .. TODO: List external libraries used (either from src/external/, or from the
424 system), whether they are required or optional, what functionality they
425 provide for Gromacs, and how to control their use.
430 In addition to the default ``all`` target, the generated build system has
431 several custom targets that are intended to be explicitly built to perform
432 various tasks (some of these may also run automatically). There are various
433 other targets as well used internally by these, but those are typically not
434 intended to be invoked directly.
437 Builds all the binaries needed by the tests and runs the tests. If some
438 types of tests are not available, shows a note to the user.
439 This is the main target intended for normal users to run the tests.
440 See :doc:`testutils`.
442 Runs a custom Python checker script to check for various source-level
443 issues. Uses Doxygen XML documentation as well as rudimentary parsing of
444 some parts of the source files.
445 This target is used as part of the Jenkins documentation job.
446 All CMake code is currently in :file:`docs/doxygen/`.
449 Runs the compiled :file:`gmx` executable to generate shell command-line
450 completion definitions. This target is only added if
451 :cmake:`GMX_BUILD_HELP` is not ``OFF``, and it is run automatically as part
452 of the default ``all`` target. See :cmake:`GMX_BUILD_HELP`.
453 All CMake code is in :file:`src/programs/`.
455 Builds include dependency graphs for the source files using :command:`dot`
457 All CMake code is in :file:`docs/doxygen/`.
460 Targets that run Doxygen to generate the documentation.
461 The ``doxygen-all`` target runs as part of the ``webpage`` target, which in
462 turn runs as part of the Jenkins documentation job.
463 All CMake code is in :file:`docs/doxygen/`.
466 Builds API documentation for gmxapi. Useful to authors of client software.
467 Documentation is generated in :file:`docs/api-user` in the build directory.
469 Extract documentation for gmxapi and GROMACS developers to
470 :file:`docs/api-dev`.
472 Runs Sphinx to generate a plain-text INSTALL file for the source package.
473 The files is generated at :file:`docs/install-guide/text/`, from where it
474 gets put at the root of the source package by CPack.
475 All CMake code is in :file:`docs/`.
477 Runs Sphinx to generate man pages for the programs.
478 Internally, also runs the compiled :file:`gmx` executable to generate the
479 input files for Sphinx.
480 All CMake code is in :file:`docs/`.
481 See :cmake:`GMX_BUILD_HELP` for information on when the man pages are
484 Runs LaTeX to generate the reference PDF manual.
485 All CMake code is in :file:`docs/manual/`.
486 See :cmake:`GMX_BUILD_MANUAL`.
488 Standard target created by CPack that builds a source package.
489 This target is used to generate the released source packages.
491 Standard target created by CTest that runs all the registered tests.
492 Note that this does not build the test binaries, only runs them, so you need
493 to first ensure that they are up-to-date.
494 See :doc:`testutils`.
496 Builds all the binaries needed by the tests (but not ``gmx``).
497 See :doc:`testutils`.
499 Collection target that runs the other documentation targets to generate the
500 full set of HTML (and linked) documentaion.
501 This target is used as part of the Jenkins documentation job.
502 All CMake code is in :file:`docs/`.
504 Runs Sphinx to generate most content for the HTML documentation (the set of
505 web pages this developer guide is also part of).
506 Internally, also runs the compiled :file:`gmx` executable to generate some
507 input files for Sphinx.
508 All CMake code is in :file:`docs/`.
510 Passing information to source code
511 ----------------------------------
513 The build system uses a few different mechanisms to influence the compilation:
515 * On the highest level, some CMake options select what files will be compiled.
516 * Some options are passed on the compiler command line using ``-D`` or
517 equivalent, such that they are available in every compilation unit. This
518 should be used with care to keep the compiler command lines manageable.
519 You can find the current set of such defines with ::
521 git grep add_definitions
523 * A few header files are generated using CMake ``configure_file()`` and
524 included in the desired source files. These files must exist for the
525 compilation to pass. Only a few files use an ``#ifdef HAVE_CONFIG_H`` to
526 protect against inclusion in case the define is not set; this is used in
527 files that may get compiled outside the main build system.
530 Contains various strings about the build environment, used mainly for
531 outputting version information to log files and when requested.
533 Contains defines for conditional compilation within source files.
534 :file:`gmxpre-config.h`
535 Included by :file:`gmxpre.h` as the first thing in every source file.
536 Should only contain defines that are required before any other header for
537 correct operation. For example, defines that affect the behavior of system
538 headers fall in this category. See Doxygen documentation for
541 All the above files get generated in :file:`src/`.
543 Additionally, the following file is generated by the build system:
545 :file:`baseversion-gen.cpp`
546 Provides definitions for declarations in :file:`baseversion_gen.h` for
547 version info output. The contents are generated either from Git version
548 info, or from static version info if not building from a git repository.