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 4.7 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 >= 4.8 and clang
73 >= 3.4 (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 >= 4.8 and
79 clang >= 3.4 (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 >= 3.4
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_DATA_INSTALL_DIR
213 Sets the directory under :file:`share/` where data files are installed.
214 The default is ``gromacs``, which puts the files under
215 file:`share/gromacs/`.
216 See :doc:`relocatable-binaries` for how this influences the build.
218 .. cmake:: GMX_DOUBLE
220 Many part of |Gromacs| are implemented in terms of "real" precision,
221 which is actually either a single- or double-precision type,
222 according to the value of this flag. Some parts of the code
223 deliberately use single- or double-precision types, and these are
224 unaffected by this setting. See reference manual for further
227 .. cmake:: GMX_RELAXED_DOUBLE_PRECISION
229 Permit a double-precision configuration to compute some quantities
230 to single-precision accuracy. Particularly on architectures where
231 only double-precision SIMD is available (e.g. Sparc machines such
232 as the K computer), it is faster to default to ``GMX_DOUBLE=ON``
233 and use SIMD than to use ``GMX_DOUBLE=OFF`` and use no
234 SIMD. However, if the user does not need full double precision,
235 then some optimizations can achieve the equivalent of
236 single-precision results (e.g. fewer Newton-Raphson iterations for
237 a reciprocal square root computation).
239 .. cmake:: GMX_EXTRAE
241 .. cmake:: GMX_EXTERNAL_BLAS
243 .. cmake:: GMX_EXTERNAL_LAPACK
245 .. cmake:: GMX_EXTERNAL_TNG
247 .. cmake:: GMX_FFT_LIBRARY
249 .. cmake:: GMX_GIT_VERSION_INFO
251 Whether to generate version information dynamically from git for each build
252 (e.g., HEAD commit hash).
253 Defaults to ``ON`` if the build is from a git repository and :command:`git`
254 is found, otherwise ``OFF``.
255 If ``OFF``, static version information from
256 :file:`cmake/gmxVersionInfo.cmake` is used.
260 .. cmake:: GMX_CLANG_CUDA
262 Use clang for compiling CUDA GPU code, both host and device.
264 .. cmake:: GMX_CUDA_CLANG_FLAGS
266 Pass additional CUDA-only compiler flags to clang using this variable.
268 .. cmake:: GMX_LIB_INSTALL_DIR
270 Sets the installation directory for libraries (default is determined by
271 standard CMake package ``GNUInstallDirs``).
272 See :doc:`relocatable-binaries` for how this influences the build.
274 .. cmake:: GMX_LOAD_PLUGINS
278 .. cmake:: GMX_OPENMP
280 .. cmake:: GMX_PREFER_STATIC_LIBS
284 .. cmake:: GMX_SOFTWARE_INVSQRT
286 .. cmake:: GMX_THREAD_MPI
288 .. cmake:: GMX_USE_RDTSCP
290 .. cmake:: GMX_USE_TNG
292 .. cmake:: GMX_VMD_PLUGIN_PATH
298 Currently, this option has no effect on the compilation or linking, since
299 there is no code outside the tests that would use :file:`libxml2`.
301 Variables affecting the ``all`` target
302 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
304 .. cmake:: BUILD_TESTING
306 Standard variable created by CTest that enables/disables all tests.
309 .. cmake:: GMX_BUILD_HELP
311 Controls handling of man pages and shell completions. Possible values:
313 ``OFF`` (default for builds from release source distribution)
314 Man pages and shell completions are not generated as part of the ``all``
315 target, and only installed if compiling from a source package.
316 ``AUTO`` (default for builds from development version)
317 Shell completions are generated by executing the :file:`gmx` binary as
318 part of the ``all`` target. If it fails, a message is printed, but the
320 Man pages need to be generated manually by invoking the ``man`` target.
321 Man pages and shell completions are installed if they have been
322 successfully generated.
324 Works the same as ``AUTO``, except that if invoking the :file:`gmx` binary
325 fails, the build fails as well.
327 .. cmake:: GMX_DEVELOPER_BUILD
329 If set ``ON``, the ``all`` target will include also the test binaries using
330 Google Test (if :cmake:`GMX_BUILD_UNITTESTS` is ``ON``).
331 Also, :cmake:`GMX_COMPILER_WARNINGS` is always enabled.
332 In the future, other developer convenience features (as well as features
333 inconvenient for a general user) can be added to the set controlled by this
336 Variables affecting special targets
337 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
339 .. cmake:: CPPCHECK_XML_OUTPUT
341 If set ``ON``, the ``cppcheck`` target generates reports for all found
342 issues in XML format. This is used by Jenkins, which parses the XML files
343 to show the issues on the web page.
344 If ``OFF`` (the default), issues are reported as plain text to standard
345 output and to a text file.
347 .. cmake:: GMX_BUILD_MANUAL
349 If set ``ON``, CMake detection for LaTeX and other prerequisites for the
350 reference PDF manual is done, and the ``manual`` target for building the
352 If ``OFF`` (the default), all detection is skipped and the manual cannot be
355 .. TODO: Consider if this is really necessary, or if we could just use
358 .. cmake:: GMX_BUILD_TARBALL
360 If set ``ON``, ``-dev`` suffix is stripped off from version strings and some
361 other version info logic is adjusted such that the man pages and other
362 documentation generated from this build is suitable for releasing (on the
363 web page and/or in the source distribution package).
366 .. cmake:: GMX_BUILD_UNITTESTS
368 If ``ON``, test binaries using Google Test are built (either as the separate
369 ``tests`` targer, or also as part of the ``all`` target, depending on
370 :cmake:`GMX_DEVELOPER_BUILD`). All dependencies required for building the
371 tests (Google Test and Google Mock frameworks, and tinyxml2) are
372 included in :file:`src/external/`.
373 Defaults to ``ON`` if :cmake:`BUILD_TESTING` is ``ON``.
375 .. cmake:: GMX_COMPACT_DOXYGEN
377 If set ``ON``, Doxygen configuration is changed to avoid generating large
378 dependency graphs, which makes it significantly faster to run Doxygen and
379 reduces disk usage. This is typically useful when developing the
380 documentation to reduce the build times.
383 .. cmake:: REGRESSIONTEST_DOWNLOAD
385 If set ``ON``, CMake will download the regression tests and extract them to
386 a local directory. :cmake:`REGRESSIONTEST_PATH` is set to the extracted
387 tests. Note that this happens during the configure phase, not during the
389 After the download is done, the variable is automatically reset to ``OFF``
390 again to avoid repeated downloads. Can be set to ``ON`` to download again.
393 .. cmake:: REGRESSIONTEST_PATH
395 Path to extracted regression test suite matching the source tree (the
396 directory containing :file:`gmxtest.pl`)
397 If set, CTest tests are generated to run the regression tests.
400 .. cmake:: SOURCE_MD5SUM
402 Sets the MD5 sum of the release tarball when generating the HTML
403 documentation. It gets inserted into the download section of the HTML
409 .. TODO: List external libraries used (either from src/external/, or from the
410 system), whether they are required or optional, what functionality they
411 provide for Gromacs, and how to control their use.
416 In addition to the default ``all`` target, the generated build system has
417 several custom targets that are intended to be explicitly built to perform
418 various tasks (some of these may also run automatically). There are various
419 other targets as well used internally by these, but those are typically not
420 intended to be invoked directly.
423 Builds all the binaries needed by the tests and runs the tests. If some
424 types of tests are not available, shows a note to the user.
425 This is the main target intended for normal users to run the tests.
426 See :doc:`testutils`.
428 Runs a custom Python checker script to check for various source-level
429 issues. Uses Doxygen XML documentation as well as rudimentary parsing of
430 some parts of the source files.
431 This target is used as part of the Jenkins documentation job.
432 All CMake code is currently in :file:`docs/doxygen/`.
435 Runs the compiled :file:`gmx` executable to generate shell command-line
436 completion definitions. This target is only added if
437 :cmake:`GMX_BUILD_HELP` is not ``OFF``, and it is run automatically as part
438 of the default ``all`` target. See :cmake:`GMX_BUILD_HELP`.
439 All CMake code is in :file:`src/programs/`.
441 Runs :command:`cppcheck` with the flags used in Jenkins for all the source
442 files. This target is directly used by the Jenkins cppcheck job.
443 All CMake code is in :file:`tests/CppCheck.cmake`.
445 Builds include dependency graphs for the source files using :command:`dot`
447 All CMake code is in :file:`docs/doxygen/`.
450 Targets that run Doxygen to generate the documentation.
451 The ``doxygen-all`` target runs as part of the ``webpage`` target, which in
452 turn runs as part of the Jenkins documentation job.
453 All CMake code is in :file:`docs/doxygen/`.
456 Runs Sphinx to generate a plain-text INSTALL file for the source package.
457 The files is generated at :file:`docs/install-guide/text/`, from where it
458 gets put at the root of the source package by CPack.
459 All CMake code is in :file:`docs/`.
461 Runs Sphinx to generate man pages for the programs.
462 Internally, also runs the compiled :file:`gmx` executable to generate the
463 input files for Sphinx.
464 All CMake code is in :file:`docs/`.
465 See :cmake:`GMX_BUILD_HELP` for information on when the man pages are
468 Runs LaTeX to generate the reference PDF manual.
469 All CMake code is in :file:`docs/manual/`.
470 See :cmake:`GMX_BUILD_MANUAL`.
472 Standard target created by CPack that builds a source package.
473 This target is used to generate the released source packages.
475 Standard target created by CTest that runs all the registered tests.
476 Note that this does not build the test binaries, only runs them, so you need
477 to first ensure that they are up-to-date.
478 See :doc:`testutils`.
480 Builds all the binaries needed by the tests (but not ``gmx``).
481 See :doc:`testutils`.
483 Collection target that runs the other documentation targets to generate the
484 full set of HTML (and linked) documentaion.
485 This target is used as part of the Jenkins documentation job.
486 All CMake code is in :file:`docs/`.
488 Runs Sphinx to generate most content for the HTML documentation (the set of
489 web pages this developer guide is also part of).
490 Internally, also runs the compiled :file:`gmx` executable to generate some
491 input files for Sphinx.
492 All CMake code is in :file:`docs/`.
494 Passing information to source code
495 ----------------------------------
497 The build system uses a few different mechanisms to influence the compilation:
499 * On the highest level, some CMake options select what files will be compiled.
500 * Some options are passed on the compiler command line using ``-D`` or
501 equivalent, such that they are available in every compilation unit. This
502 should be used with care to keep the compiler command lines manageable.
503 You can find the current set of such defines with ::
505 git grep add_definitions
507 * A few header files are generated using CMake ``configure_file()`` and
508 included in the desired source files. These files must exist for the
509 compilation to pass. Only a few files use an ``#ifdef HAVE_CONFIG_H`` to
510 protect against inclusion in case the define is not set; this is used in
511 files that may get compiled outside the main build system.
514 Contains various strings about the build environment, used mainly for
515 outputting version information to log files and when requested.
517 Contains defines for conditional compilation within source files.
518 :file:`gmxpre-config.h`
519 Included by :file:`gmxpre.h` as the first thing in every source file.
520 Should only contain defines that are required before any other header for
521 correct operation. For example, defines that affect the behavior of system
522 headers fall in this category. See Doxygen documentation for
525 All the above files get generated in :file:`src/`.
527 Additionally, the following file is generated by the build system:
529 :file:`baseversion-gen.c`
530 Provides definitions for declarations in :file:`baseversion-gen.h` for
531 version info output. The contents are generated either from Git version
532 info, or from static version info if not building from a git repository.