.. highlight:: bash
Build system overview
=====================
The |Gromacs| build system uses CMake (version
|CMAKE_MINIMUM_REQUIRED_VERSION| or newer is required) to generate the
actual build system for the build tool chosen 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 :file:`.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 9 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 :ref:`gmx mdrun`, but can
be useful for the tools.
**TSAN**
Builds |Gromacs| for use with ThreadSanitizer in gcc and clang
(https://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 AddressSanitizer in gcc and
clang (https://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 MemorySanitizer in clang
(https://clang.llvm.org/docs/MemorySanitizer.html) to detect
reads of uninitialized 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``) includes 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.
.. todo::
Figure out where to document basic variables intended for user
consumption, and how does it relate to documentation here.
.. todo::
Document the remaining variables below, and identify any variables
missing from the list.
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 :samp:`CMAKE_C_FLAGS_{buildtype}`/:samp:`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:
.. cmake:: 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
:command:`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
:file:`cmake/gmxCFlags.cmake`.
Code that sets the specific flags (e.g., SIMD flags) is in the main
:file:`CMakeLists.txt`; search for :cmake:`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
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. cmake:: GMX_BROKEN_CALLOC
Enable emulation of ``calloc`` via ``malloc``/``memset``.
Only needed on machines with a broken ``calloc(3)``, e.g. in ``-lgmalloc``
on Cray XT3.
Defaults to ``OFF``, and there should not be any need to change this unless
you are sure it is required.
.. cmake:: GMX_BUILD_FOR_COVERAGE
Special variable set ``ON`` by CI 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.
.. todo:: This could likely be replaced by a (yet another) build type.
.. cmake:: GMX_BUILD_OWN_FFTW
If set ``ON``, |Gromacs| build system will download and build FFTW from source
automatically. Not supported on Windows or with ``ninja`` build system.
In complicated scenarios (e.g., when cross-compiling or using a toolchain
file), we recommend not relying on this feature and building FFTW manually.
.. cmake:: GMX_BUILD_SHARED_EXE
Build executables as shared binaries. If not set, this disables ``-rpath`` and dynamic
linker flags in an attempt to build a static binary, but this may require setting up
the toolchain properly and making appropriate libraries available. Defaults to ``ON``.
.. cmake:: GMX_COMPILER_WARNINGS
If set ``ON``, various compiler warnings are enabled for compilers that
CI uses for verification.
Defaults to ``OFF`` when building from a source tarball so that users
compiling with versions not tested in CI 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``.
.. cmake:: 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 :doc:`/user-guide/mdrun-performance` for the description of
subcounters which are available.
Defaults to ``OFF``.
.. cmake:: 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.
.. cmake:: 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 :doc:`relocatable-binaries` for how this influences the build.
.. cmake:: 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
:doc:`Mixed or Double precision `
for further information.
.. cmake:: GMX_EXTRAE
Add support for tracing using `Extrae `_.
.. cmake:: GMX_EXTERNAL_BLAS
If not set (the default), CMake will first try to use an external BLAS library,
and, if unsuccessful, fall back to using the one bundled with |Gromacs|.
If set to ``OFF``, CMake will use the bundled one immediately.
If set to ``ON``, CMake will use the external one, and raise an error if it is not found.
.. cmake:: GMX_EXTERNAL_LAPACK
See ``GMX_EXTERNAL_BLAS``.
.. cmake:: GMX_EXTERNAL_TNG
Use external TNG library for trajectory-file handling. Default: ``OFF``.
.. cmake:: GMX_FFT_LIBRARY
Choose the CPU FFT library to use. Possible values: ``fftw``, ``mkl``, ``fftpack``.
The default selection depends on the compiler and build type.
.. cmake:: 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 :command:`git`
is found, otherwise ``OFF``.
If ``OFF``, static version information from
:file:`cmake/gmxVersionInfo.cmake` is used.
.. cmake:: GMX_GPU
Choose the backend for GPU offload. Possible values: ``CUDA``, ``OpenCL``, ``SYCL``.
Please see the :ref:`Installation guide ` for more information.
.. cmake:: GMX_CLANG_CUDA
Use clang for compiling CUDA GPU code, both host and device.
Please see the :ref:`Installation guide ` for more information.
.. cmake:: GMX_CUDA_CLANG_FLAGS
Pass additional CUDA-only compiler flags to clang using this variable.
.. cmake:: CMAKE_INSTALL_LIBDIR
Sets the installation directory for libraries (default is determined by
standard CMake package ``GNUInstallDirs``).
See :doc:`relocatable-binaries` for how this influences the build.
.. cmake:: GMX_USE_PLUGINS
Enable support for dynamic plugins (e.g. VMD-supported file formats).
Default: ``OFF``.
.. cmake:: GMX_MPI
Enable MPI (not thread-MPI) support for inter-node parallelism. Defaults to ``OFF``.
Please see the :ref:`Installation guide ` for more information.
.. cmake:: GMX_OPENMP
Enable OpenMP support. Default is ``ON``.
.. cmake:: GMX_PREFER_STATIC_LIBS
Prefer statically linking to external libraries. Defaults to ``OFF``, unless
``GMX_BUILD_SHARED_EXE`` is disabled.
.. cmake:: GMX_SIMD
Choose SIMD instruction set to use. Default is: ``Auto`` (best one for the current CPU).
Please see the :ref:`Installation guide ` for more information.
.. cmake:: GMX_THREAD_MPI
Enable thread-MPI support for inter-node parallelism. Defaults to ``ON``.
.. cmake:: GMX_USE_RDTSCP
Use low-latency ``RDTSCP`` instruction for x86 CPU-based timers for mdrun execution.
Ignored on non-x86 machines. Might need to be set to ``OFF`` when compiling for
for heterogeneous environments or a very old x86 CPU.
.. cmake:: GMX_USE_TNG
Use the TNG library for trajectory I/O. Defaults to ``ON``.
.. cmake:: GMX_VMD_PLUGIN_PATH
Path to VMD plugins for molfile I/O. Only used when ``GMX_USE_PLUGINS`` is enabled.
Variables affecting the ``all`` target
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. cmake:: BUILD_TESTING
Standard variable created by CTest that enables/disables all tests.
Defaults to ``ON``.
.. cmake:: 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 :file:`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 :file:`gmx` binary
fails, the build fails as well.
.. cmake:: GMX_DEVELOPER_BUILD
If set ``ON``, the ``all`` target will include also the test binaries using
Google Test (if :cmake:`GMX_BUILD_UNITTESTS` is ``ON``).
Also, :cmake:`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.
.. cmake:: 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 11.0.* is supported. Others might miss tests or give false positives.
It is run automatically in GitLab CI 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 -DCMAKE_BUILD_TYPE=Debug``.
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 issues identified, clang-tidy should be run separately (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 '.*' '(?`_.
.. cmake:: GMX_INSTALL_NBLIB_API
If set to ``ON`` (default, when :cmake:`BUILD_SHARED_LIBS` on non-Windows platforms),
build and install the :file:`libnb_gmx` and :file:`nblib/` headers.
See :ref:`nblib`.
.. cmake:: GMXAPI
If set ``ON`` (default, when :cmake:`BUILD_SHARED_LIBS` on non-Windows platforms),
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.
.. cmake:: 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.
.. todo:: Consider if this is really necessary, or if we could just use
GMX_DEVELOPER_BUILD.
.. cmake:: 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``.
.. cmake:: GMX_BUILD_UNITTESTS
If ``ON``, test binaries using Google Test are built (either as the separate
``tests`` target, or also as part of the ``all`` target, depending on
:cmake:`GMX_DEVELOPER_BUILD`). All dependencies required for building the
tests (Google Test and Google Mock frameworks, and tinyxml2) are
included in :file:`src/external/`.
Defaults to ``ON`` if :cmake:`BUILD_TESTING` is ``ON``.
.. cmake:: 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``.
.. cmake:: REGRESSIONTEST_DOWNLOAD
If set ``ON``, CMake will download the regression tests and extract them to
a local directory. :cmake:`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``.
.. cmake:: REGRESSIONTEST_PATH
Path to extracted regression test suite matching the source tree (the
directory containing :file:`gmxtest.pl`)
If set, CTest tests are generated to run the regression tests.
Defaults to empty.
.. cmake:: 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
------------------
.. todo::
List external libraries used (either from src/external/, or from the
system), whether they are required or optional, what functionality they
provide for |Gromacs|, and how to control their use.
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 :doc:`testutils`.
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 CI.
All CMake code is currently in :file:`docs/doxygen/`.
See :doc:`gmxtree`.
completion
Runs the compiled :file:`gmx` executable to generate shell command-line
completion definitions. This target is only added if
:cmake:`GMX_BUILD_HELP` is not ``OFF``, and it is run automatically as part
of the default ``all`` target. See :cmake:`GMX_BUILD_HELP`.
All CMake code is in :file:`src/programs/`.
dep-graphs*
Builds include dependency graphs for the source files using :command:`dot`
from graphviz.
All CMake code is in :file:`docs/doxygen/`.
See :doc:`gmxtree`.
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 CI.
All CMake code is in :file:`docs/doxygen/`.
See :doc:`doxygen`.
gmxapi-cppdocs
Builds API documentation for gmxapi. Useful to authors of client software.
Documentation is generated in :file:`docs/api-user` in the build directory.
gmxapi-cppdocs-dev
Extract documentation for gmxapi and |Gromacs| developers to
:file:`docs/api-dev`.
install-guide
Runs Sphinx to generate a plain-text INSTALL file for the source package.
The files is generated at :file:`docs/install-guide/text/`, from where it
gets put at the root of the source package by CPack.
All CMake code is in :file:`docs/`.
man
Runs Sphinx to generate man pages for the programs.
Internally, also runs the compiled :file:`gmx` executable to generate the
input files for Sphinx.
All CMake code is in :file:`docs/`.
See :cmake:`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 :file:`docs/manual/`.
See :cmake:`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 :doc:`testutils`.
tests
Builds all the binaries needed by the tests (but not ``gmx``).
See :doc:`testutils`.
webpage
Collection target that runs the other documentation targets to generate the
full set of HTML (and linked) documentation.
This target is used as part of the CI.
All CMake code is in :file:`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 :file:`gmx` executable to generate some
input files for Sphinx.
All CMake code is in :file:`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.
:file:`buildinfo.h`
Contains various strings about the build environment, used mainly for
outputting version information to log files and when requested.
:file:`config.h`
Contains defines for conditional compilation within source files.
:file:`gmxpre-config.h`
Included by :file:`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
:file:`gmxpre.h`.
The above files are available through the INTERFACE_INCLUDE_DIR of
the ``common`` CMake target. I.e. to ``#include "config.h"``, be sure to
``target_link_libraries(mymodule PRIVATE common)``
Additionally, the following file is generated by the build system:
:file:`baseversion-gen.cpp`
Provides definitions for declarations in :file:`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.