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_INSTALL_DATASUBDIR
213 Sets the subdirectory under CMAKE_INSTALL_DATADIR where GROMACS-specific
214 read-only architecture-independent data files are installed. The default
215 is ``gromacs``, which means the files will go under ``share/gromacs``.
216 To alter the ``share`` part, change CMAKE_INSTALL_DATADIR.
217 See :doc:`relocatable-binaries` for how this influences the build.
219 .. cmake:: GMX_DOUBLE
221 Many part of |Gromacs| are implemented in terms of "real" precision,
222 which is actually either a single- or double-precision type,
223 according to the value of this flag. Some parts of the code
224 deliberately use single- or double-precision types, and these are
225 unaffected by this setting. See reference manual for further
228 .. cmake:: GMX_RELAXED_DOUBLE_PRECISION
230 Permit a double-precision configuration to compute some quantities
231 to single-precision accuracy. Particularly on architectures where
232 only double-precision SIMD is available (e.g. Sparc machines such
233 as the K computer), it is faster to default to ``GMX_DOUBLE=ON``
234 and use SIMD than to use ``GMX_DOUBLE=OFF`` and use no
235 SIMD. However, if the user does not need full double precision,
236 then some optimizations can achieve the equivalent of
237 single-precision results (e.g. fewer Newton-Raphson iterations for
238 a reciprocal square root computation).
240 .. cmake:: GMX_EXTRAE
242 .. cmake:: GMX_EXTERNAL_BLAS
244 .. cmake:: GMX_EXTERNAL_LAPACK
246 .. cmake:: GMX_EXTERNAL_TNG
248 .. cmake:: GMX_FFT_LIBRARY
250 .. cmake:: GMX_GIT_VERSION_INFO
252 Whether to generate version information dynamically from git for each build
253 (e.g., HEAD commit hash).
254 Defaults to ``ON`` if the build is from a git repository and :command:`git`
255 is found, otherwise ``OFF``.
256 If ``OFF``, static version information from
257 :file:`cmake/gmxVersionInfo.cmake` is used.
261 .. cmake:: GMX_CLANG_CUDA
263 Use clang for compiling CUDA GPU code, both host and device.
265 .. cmake:: GMX_CUDA_CLANG_FLAGS
267 Pass additional CUDA-only compiler flags to clang using this variable.
269 .. cmake:: CMAKE_INSTALL_LIBDIR
271 Sets the installation directory for libraries (default is determined by
272 standard CMake package ``GNUInstallDirs``).
273 See :doc:`relocatable-binaries` for how this influences the build.
275 .. cmake:: GMX_LOAD_PLUGINS
279 .. cmake:: GMX_OPENMP
281 .. cmake:: GMX_PREFER_STATIC_LIBS
285 .. cmake:: GMX_SOFTWARE_INVSQRT
287 .. cmake:: GMX_THREAD_MPI
289 .. cmake:: GMX_USE_RDTSCP
291 .. cmake:: GMX_USE_TNG
293 .. cmake:: GMX_VMD_PLUGIN_PATH
299 Currently, this option has no effect on the compilation or linking, since
300 there is no code outside the tests that would use :file:`libxml2`.
302 Variables affecting the ``all`` target
303 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
305 .. cmake:: BUILD_TESTING
307 Standard variable created by CTest that enables/disables all tests.
310 .. cmake:: GMX_BUILD_HELP
312 Controls handling of man pages and shell completions. Possible values:
314 ``OFF`` (default for builds from release source distribution)
315 Man pages and shell completions are not generated as part of the ``all``
316 target, and only installed if compiling from a source package.
317 ``AUTO`` (default for builds from development version)
318 Shell completions are generated by executing the :file:`gmx` binary as
319 part of the ``all`` target. If it fails, a message is printed, but the
321 Man pages need to be generated manually by invoking the ``man`` target.
322 Man pages and shell completions are installed if they have been
323 successfully generated.
325 Works the same as ``AUTO``, except that if invoking the :file:`gmx` binary
326 fails, the build fails as well.
328 .. cmake:: GMX_DEVELOPER_BUILD
330 If set ``ON``, the ``all`` target will include also the test binaries using
331 Google Test (if :cmake:`GMX_BUILD_UNITTESTS` is ``ON``).
332 Also, :cmake:`GMX_COMPILER_WARNINGS` is always enabled.
333 In the future, other developer convenience features (as well as features
334 inconvenient for a general user) can be added to the set controlled by this
337 Variables affecting special targets
338 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
340 .. cmake:: CPPCHECK_XML_OUTPUT
342 If set ``ON``, the ``cppcheck`` target generates reports for all found
343 issues in XML format. This is used by Jenkins, which parses the XML files
344 to show the issues on the web page.
345 If ``OFF`` (the default), issues are reported as plain text to standard
346 output and to a text file.
348 .. cmake:: GMX_BUILD_MANUAL
350 If set ``ON``, CMake detection for LaTeX and other prerequisites for the
351 reference PDF manual is done, and the ``manual`` target for building the
353 If ``OFF`` (the default), all detection is skipped and the manual cannot be
356 .. TODO: Consider if this is really necessary, or if we could just use
359 .. cmake:: GMX_BUILD_TARBALL
361 If set ``ON``, ``-dev`` suffix is stripped off from version strings and some
362 other version info logic is adjusted such that the man pages and other
363 documentation generated from this build is suitable for releasing (on the
364 web page and/or in the source distribution package).
367 .. cmake:: GMX_BUILD_UNITTESTS
369 If ``ON``, test binaries using Google Test are built (either as the separate
370 ``tests`` targer, or also as part of the ``all`` target, depending on
371 :cmake:`GMX_DEVELOPER_BUILD`). All dependencies required for building the
372 tests (Google Test and Google Mock frameworks, and tinyxml2) are
373 included in :file:`src/external/`.
374 Defaults to ``ON`` if :cmake:`BUILD_TESTING` is ``ON``.
376 .. cmake:: GMX_COMPACT_DOXYGEN
378 If set ``ON``, Doxygen configuration is changed to avoid generating large
379 dependency graphs, which makes it significantly faster to run Doxygen and
380 reduces disk usage. This is typically useful when developing the
381 documentation to reduce the build times.
384 .. cmake:: REGRESSIONTEST_DOWNLOAD
386 If set ``ON``, CMake will download the regression tests and extract them to
387 a local directory. :cmake:`REGRESSIONTEST_PATH` is set to the extracted
388 tests. Note that this happens during the configure phase, not during the
390 After the download is done, the variable is automatically reset to ``OFF``
391 again to avoid repeated downloads. Can be set to ``ON`` to download again.
394 .. cmake:: REGRESSIONTEST_PATH
396 Path to extracted regression test suite matching the source tree (the
397 directory containing :file:`gmxtest.pl`)
398 If set, CTest tests are generated to run the regression tests.
401 .. cmake:: SOURCE_MD5SUM
403 Sets the MD5 sum of the release tarball when generating the HTML
404 documentation. It gets inserted into the download section of the HTML
410 .. TODO: List external libraries used (either from src/external/, or from the
411 system), whether they are required or optional, what functionality they
412 provide for Gromacs, and how to control their use.
417 In addition to the default ``all`` target, the generated build system has
418 several custom targets that are intended to be explicitly built to perform
419 various tasks (some of these may also run automatically). There are various
420 other targets as well used internally by these, but those are typically not
421 intended to be invoked directly.
424 Builds all the binaries needed by the tests and runs the tests. If some
425 types of tests are not available, shows a note to the user.
426 This is the main target intended for normal users to run the tests.
427 See :doc:`testutils`.
429 Runs a custom Python checker script to check for various source-level
430 issues. Uses Doxygen XML documentation as well as rudimentary parsing of
431 some parts of the source files.
432 This target is used as part of the Jenkins documentation job.
433 All CMake code is currently in :file:`docs/doxygen/`.
436 Runs the compiled :file:`gmx` executable to generate shell command-line
437 completion definitions. This target is only added if
438 :cmake:`GMX_BUILD_HELP` is not ``OFF``, and it is run automatically as part
439 of the default ``all`` target. See :cmake:`GMX_BUILD_HELP`.
440 All CMake code is in :file:`src/programs/`.
442 Runs :command:`cppcheck` with the flags used in Jenkins for all the source
443 files. This target is directly used by the Jenkins cppcheck job.
444 All CMake code is in :file:`tests/CppCheck.cmake`.
446 Builds include dependency graphs for the source files using :command:`dot`
448 All CMake code is in :file:`docs/doxygen/`.
451 Targets that run Doxygen to generate the documentation.
452 The ``doxygen-all`` target runs as part of the ``webpage`` target, which in
453 turn runs as part of the Jenkins documentation job.
454 All CMake code is in :file:`docs/doxygen/`.
457 Runs Sphinx to generate a plain-text INSTALL file for the source package.
458 The files is generated at :file:`docs/install-guide/text/`, from where it
459 gets put at the root of the source package by CPack.
460 All CMake code is in :file:`docs/`.
462 Runs Sphinx to generate man pages for the programs.
463 Internally, also runs the compiled :file:`gmx` executable to generate the
464 input files for Sphinx.
465 All CMake code is in :file:`docs/`.
466 See :cmake:`GMX_BUILD_HELP` for information on when the man pages are
469 Runs LaTeX to generate the reference PDF manual.
470 All CMake code is in :file:`docs/manual/`.
471 See :cmake:`GMX_BUILD_MANUAL`.
473 Standard target created by CPack that builds a source package.
474 This target is used to generate the released source packages.
476 Standard target created by CTest that runs all the registered tests.
477 Note that this does not build the test binaries, only runs them, so you need
478 to first ensure that they are up-to-date.
479 See :doc:`testutils`.
481 Builds all the binaries needed by the tests (but not ``gmx``).
482 See :doc:`testutils`.
484 Collection target that runs the other documentation targets to generate the
485 full set of HTML (and linked) documentaion.
486 This target is used as part of the Jenkins documentation job.
487 All CMake code is in :file:`docs/`.
489 Runs Sphinx to generate most content for the HTML documentation (the set of
490 web pages this developer guide is also part of).
491 Internally, also runs the compiled :file:`gmx` executable to generate some
492 input files for Sphinx.
493 All CMake code is in :file:`docs/`.
495 Passing information to source code
496 ----------------------------------
498 The build system uses a few different mechanisms to influence the compilation:
500 * On the highest level, some CMake options select what files will be compiled.
501 * Some options are passed on the compiler command line using ``-D`` or
502 equivalent, such that they are available in every compilation unit. This
503 should be used with care to keep the compiler command lines manageable.
504 You can find the current set of such defines with ::
506 git grep add_definitions
508 * A few header files are generated using CMake ``configure_file()`` and
509 included in the desired source files. These files must exist for the
510 compilation to pass. Only a few files use an ``#ifdef HAVE_CONFIG_H`` to
511 protect against inclusion in case the define is not set; this is used in
512 files that may get compiled outside the main build system.
515 Contains various strings about the build environment, used mainly for
516 outputting version information to log files and when requested.
518 Contains defines for conditional compilation within source files.
519 :file:`gmxpre-config.h`
520 Included by :file:`gmxpre.h` as the first thing in every source file.
521 Should only contain defines that are required before any other header for
522 correct operation. For example, defines that affect the behavior of system
523 headers fall in this category. See Doxygen documentation for
526 All the above files get generated in :file:`src/`.
528 Additionally, the following file is generated by the build system:
530 :file:`baseversion-gen.c`
531 Provides definitions for declarations in :file:`baseversion-gen.h` for
532 version info output. The contents are generated either from Git version
533 info, or from static version info if not building from a git repository.