Details on the deal.II configuration and build system

The deal.II README file gives an overview over the basics of configuring and building the deal.II library. This page provides more details about using the deal.II CMake build system.

  1. Operating cmake
    1. Manipulating the cache
    2. ccmake and special build targets
    3. Shortcuts
  2. Configuring and Building deal.II
    1. Primary build targets
    2. Information about current configuration
    3. Out-of-source versus in-source builds
    4. CMake Generators
    5. Installation
  3. Configuration options
    1. Feature configuration
    2. Autoconfiguration
    3. External library locations
    4. Manual override
    5. Component selection
    6. Build configuration
    7. Selecting a compiler
    8. Installation
  4. Initial cache file and advanced options
  5. Compiling only certain parts

Operating cmake

When configuring deal.II by running cmake, the cmake program creates a cache in the current (build) directory that contains the values of all (cached) variables that had previously been passed as command line arguments, been found through running tests, or had otherwise been set.

On a subsequent call to cmake, e.g. to change the configuration or due to a callback from the build system because some configuration file (the CMakeLists.txt and cmake/<..>.cmake files) has changed, cmake will only run whatever tests are necessary; values for variables that are already in the cache are not re-evaluated. This means that calling cmake a second time without any arguments at all in a situation like this

mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=/path/install/dir ../deal.II
cmake ../deal.II
has no effect: In particular, the CMAKE_INSTALL_PREFIX specified on the first invocation of cmake is cached and therefore still valid after the second invocation of cmake This is different from the way the autoconf/configure mechanism worked.

The cache has an important reason: one can modify all sort of configuration parameters and thereby interact with the configuration system in rather powerful (and, possibly, destructive) ways. For example, the following commands

mkdir build
cd build
cmake  ../deal.II
ccmake
first configure a bare-bone setup and then call the ccmake program -- an interactive editor for the cached variables. Similarly,
mkdir build
cd build
cmake  ../deal.II
cmake -D<OPTION>=<VALUE> [...] ../deal.II
sets a variable the second time around without destroying all the configuration that has happened the first time around. Likewise,
mkdir build
cd build
cmake  ../deal.II
cmake -DDEAL_II_WITH_METIS=OFF .
cmake -DDEAL_II_WITH_TRILINOS=ON -DTRILINOS_DIR=/path/to/trilinos .
switches off support for the METIS library that may have been automatically detected during the first invocation of cmake and enables support for Trilinos by enabling DEAL_II_WITH_TRILINOS and setting TRILINOS_DIR.

Manipulating the cache

A cached variable can be set on the command line via

cmake -D<VARIABLE>=<VALUE> .
Cached variables can be removed from the cache via
cmake -U<VARIABLE> .
It is possible to use -U together with a globbing expression. E.g. to remove the current feature configuration and rerun the autodetection one can invoke
cmake -U"DEAL_II_WITH_*" .

ccmake and special build targets

A very convenient way to alter the configuration is to use the graphical user interface ccmake to the variables cmake stores upon running. It can be invoked via

ccmake .
or by
make edit_cache
A reconfiguration (without editing the cache) can be run via
make rebuild_cache

Shortcuts

All variables starting with WITH_ will be automatically renamed to DEAL_II_WITH_*. So, it suffices to specify

cmake -DWITH_MPI=ON <...>
instead of the longer
cmake -DDEAL_II_WITH_MPI=ON <...>
The same holds for all variables starting with COMPONENT_ and all individual component names: DOCUMENTATION, EXAMPLES and PARAMETER_GUI (which will be expanded to the full DEAL_II_COMPONENT_* variable name).

Configuring and Building deal.II

This section provides some further details and advanced topics with respect to configuration and building that is not covered in the README.

Primary build targets

The current list of primary build targets can be queried via make info:

###
#
#  The following targets are available (invoke by $ make <target>):
#
#    all            - compile the library and all enabled components
#    clean          - remove all generated files
#    install        - install into CMAKE_INSTALL_PREFIX
#
#    info           - print this help message
#    help           - print a list of valid top level targets
#
#    edit_cache     - run ccmake for changing (cached) configuration variables
#                     and reruns the configure and generate phases of CMake
#    rebuild_cache  - rerun the configure and generate phases of CMake
#
#    compat_files   - build and install component 'compat_files'
#    documentation  - build and install component 'documentation'
#    examples       - build and install component 'examples'
#    library        - build and install component 'library'
#    parameter_gui  - build and install component 'parameter_gui'
#    package        - build binary package
#
#    test           - run a minimal set of tests
#
#    setup_tests    - set up testsuite subprojects
#    prune_tests    - remove all testsuite subprojects
#
###

Information about current configuration

A configuration run of cmake (or ccmake) writes a short summary of the current configuration into CMAKE_BUILD_DIR/summary.log:

###
#
#  deal.II configuration:
#        CMAKE_BUILD_TYPE:       DebugRelease
#        BUILD_SHARED_LIBS:      ON
#        CMAKE_INSTALL_PREFIX:   /tmp/deal.II/install
#        CMAKE_SOURCE_DIR:       /tmp/deal.II/deal.II (Version 8.1.pre)
#        CMAKE_BINARY_DIR:       /tmp/deal.II/build
#        CMAKE_CXX_COMPILER:     GNU 4.7.3 on platform Linux x86_64
#                                /usr/bin/c++
#
#  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION = ON):
#      ( DEAL_II_WITH_64BIT_INDICES = OFF )
#        DEAL_II_WITH_ARPACK set up with external dependencies
#        DEAL_II_WITH_BOOST set up with external dependencies
#        [...]
#
#  Component configuration:
#      ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
#        DEAL_II_COMPONENT_EXAMPLES
#      ( DEAL_II_COMPONENT_PARAMETER_GUI = OFF )
#
#  Detailed information (compiler flags, feature configuration) can be found in detailed.log
#
#  Run  $ make info  to print a help message with a list of top level targets
#
###
This summary is also printed at the end of the configuration phase. It tells you about build and install directory locations, feature configuration (whether a feature is enabled with external/internal dependencies, disabled or forced) and component configuration. A more detailed version can be found in CMAKE_BUILD_DIR/detailed.log that also includes detailed information about feature configuration, e.g.
#        DEAL_II_WITH_BOOST set up with external dependencies
#            BOOST_VERSION = 1.52.0
#            BOOST_DIR =
#            Boost_INCLUDE_DIRS = /usr/include
#            Boost_LIBRARIES = /usr/lib64/libboost_serialization-mt.so;/usr/lib64/libboost_system-mt.so;
# [...]
If this information is not sufficient, you might want to have a look at the following files in CMAKE_BUILD_DIR

Out-of-source versus in-source builds

A so called out-of-source build is a setup where the build directory (the directory containing intermediate and generated files) is different from the source directory (the directory containing the source code). With CMake an out-of-source build is set up by invoking cmake (or ccmake) from the designated build directory, so for example (a build directory under the source directory):

$ mkdir build
$ cd build
$ cmake ..
The big advantage is that source files and intermediate files are strictly separated (highly desired for version control) and that you can have multiple build directories (with different configuration) at the same time.

Note: However, under rare occasions an in-source build might be useful or needed , so it is supported

$ cmake .
But we highly discourage it!

CMake Generators

Cmake is a Makefile Generator. This allows to switch the generator that is used to something different. If you for example want to automatically generate an Eclipse project of deal.II, you can run

$ cmake -G"Eclipse CDT4 - Unix Makefiles" [...]
and load up the build directory as a project directly into Eclipse. Have a look at the Wiki for more information.

An interesting alternative to (GNU) Make might also be Ninja. Configure via

$ cmake -GNinja [...]
and run ninja instead of make.

Installation

It is not necessary to install the library in order to use deal.II. Invoking the all or library target will compile the library and set up all necessary configuration in the build directory so that external projects can directly use it. However, we strongly recommend to proceed in the way explained in the README and install the library to a designated install directory (different from source and build directory).

For installing the library it is necessary to set the CMake variable CMAKE_INSTALL_PREFIX to the designated install directory. You can do this by invoking cmake together with -DCMAKE_INSTALL_PREFIX=<...> or by invoking ccmake.

Note: When you don't install deal.II to an install directory and use it directly from a build directory, both, the build and source directories have to be kept.

Note: It is not necessary for the source, build and or install directory to be different. All combinations are supported.

Install a single component

If you want to only generate, compile and install a specific component (most notably the documentation) you can use one of the following top level targets:

documentation  - builds and installs the 'documentation' component
examples       - builds and installs the 'examples' component
library        - builds and installs the 'library' component
parameter_gui  - builds and installs the 'parameter_gui' component

Configuration options

The various configuration options of the deal.II library are organized in three categories: feature, component, and build/install configuration.

Feature configuration

deal.II provides (optional) interfaces to quite a number of external libraries as well as multiple versions of C++. All of these options are represented by cmake variables that may be set to either ON or OFF. By default, deal.II's CMake build scripts will attempt to find the newest C++ version available by checking which language version flags work with the detected compiler. For example: if CMake detects GCC 5.1 or Clang 3.6, deal.II will be compiled in C++14 mode unless either C++14 or C++11 is explicitly disabled. Another example: if DEAL_II_WITH_CXX11=ON is passed to CMake, then deal.II will check if the compiler supports enough parts of the C++11 and C++14 language standards. CMake will not fail in this example just because the compiler does not support C++14, but CMake will fail if the compiler does not support enough of C++11. The remaining flags are set to ON if an external package is found or to OFF otherwise. By explicitly setting it to off either on the command line or using ccmake, you can prevent deal.II from using an external package, even if it is found.

Specifically, the following variables exist (the list may grow over time, but names are standardized):

DEAL_II_WITH_64BIT_INDICES
DEAL_II_WITH_ARPACK
DEAL_II_WITH_BOOST
DEAL_II_WITH_BZIP2
DEAL_II_WITH_CXX11
DEAL_II_WITH_CXX14
DEAL_II_WITH_HDF5
DEAL_II_WITH_LAPACK
DEAL_II_WITH_METIS
DEAL_II_WITH_MPI
DEAL_II_WITH_MUPARSER
DEAL_II_WITH_NETCDF
DEAL_II_WITH_OPENCASCADE
DEAL_II_WITH_P4EST
DEAL_II_WITH_PETSC
DEAL_II_WITH_SLEPC
DEAL_II_WITH_THREADS
DEAL_II_WITH_TRILINOS
DEAL_II_WITH_UMFPACK
DEAL_II_WITH_ZLIB
They all have standard meaning with the exception of two:

If enabled, each of the features above will usually add one or more dependencies to external or 'bundled' (i.e. bundled with deal.II and residing under bundled/) libraries.

Additionally, the variable

DEAL_II_CXX_VERSION_FLAG
may be set to specify the C++ language version flag passed to the compiler.

There are some options to determine the behavior of the dependency resolution.

Autoconfiguration

As long as DEAL_II_WITH_<FEATURE> is not explicitly set to ON or OFF in the cache it will be automatically configured. If a toggle DEAL_II_WITH_<FEATURE> is defined it won't be altered. This means that the very first configuration run will set all available features to ON and the rest to OFF. In all subsequent configuration steps DEAL_II_WITH_<FEATURE> has to be changed by hand, see the previous section.

This behavior can be controlled via several variables:

External library locations

External libraries will be searched depending on hints in the following order:

  1. Paths specified via CMAKE_PREFIX_PATH take precedence, e.g. with

    make -DCMAKE_PREFIX_PATH=~/workspace/local ../deal.II
    
    libraries from ~/workspace/local will be preferred for dependency resolution.

  2. Hints given by <library>_DIR via command line or environment for some libraries:

    make -DP4EST_DIR=~/workspace/p4est-install/ ../deal.II
    
    or
    export P4EST_DIR=~/workspace/p4est-install/
    cmake ../deal.II
    
    where -D<library>_DIR takes precedence over environment.

    Currently, the following variables will be considered:

    ARPACK_DIR,
    BOOST_DIR,
    HDF5_DIR,
    LAPACK_DIR (and BLAS_DIR),
    METIS_DIR,
    MUPARSER_DIR,
    P4EST_DIR (and SC_DIR),
    PETSC_DIR and PETSC_ARCH (forming ${PETSC_DIR}/${PETSC_ARCH}),
    SLEPC_DIR (forming ${SLEPC_DIR}/${PETSC_ARCH}),
    TBB_DIR,
    TRILINOS_DIR,
    UMFPACK_DIR and SUITESPARSE_DIR (AMD_DIR, CHOLMOD_DIR, COLAMD_DIR, SUITESPARSECONFIG_DIR)
    

  3. The default system locations for libraries and includes.

Alternatively, cached variables set by the Find<Module> mechanism may be set, hinted or overwritten directly (variable names are highly dependent on the actual library). You can get a list via

make edit_cache
and entering advanced configuration mode by pressing [t]. Variables that could not be determined are suffixed with -NOTFOUND and may be set by hand.

Library conflicts

Caveat: if you have a set of standard libraries in the default location, say /usr/lib and a set of private versions of the same libraries, for instance because you need different revisions sometimes, in your own library directory, you may receive an error message of the form:

CMake Warning at source/CMakeLists.txt:65 (ADD_LIBRARY):
  Cannot generate a safe runtime search path for target deal_II.g because
  files in some directories may conflict with libraries in implicit
  directories:

    runtime library [libtbb.so.2] in /usr/lib may be hidden by files in:
      /my/private/lib

  Some of these libraries may not be found correctly.

This is not a problem of CMake or deal.II, but rather a general Linux problem. In order to fix this, you have two options:

  1. Choose all libraries either from your private directory or from the standard one.
  2. Install all your private library versions in different directories.

Manual override

Warning: Do not do this unless absolutely necessary!

It is possible to override the CMake find mechanism for external libraries manually. This is useful if a non standard library (e.g. BLAS or LAPACK) should be used but cannot be found by the FIND_PACKAGE(...) mechanism. In this case you can set by hand:

cmake -D<feature>_FOUND=true \
      -D<feature>_LIBRARIES="library;and;complete;link;interface" \
    ( -D<feature>_INCLUDE_DIRS="semicolon;separated;list;of;include;dirs" \
      -D<feature>_LINKER_FLAGS="..." \
      -D<feature>_<...depending on library...> )
The first define ensures that cmake does not call the corresponding Find<lib>.cmake module. Therefore, all information that would be otherwise exported by the module must be specified by hand. (See the config.sample file for a detailed list of valid variables per feature.)

An example of use is to select BLAS and LAPACK manually from a PETSc configuration: (Here, these libraries have been compiled with the gfortran compiler and need its support library):

cmake -DLAPACK_FOUND=true \
      -DLAPACK_LIBRARIES="/tmp/petsc-3.3-p6/arch-linux2-c-debug/lib/libflapack.a;/tmp/petsc-3.3-p6/arch-linux2-c-debug/lib/libfblas.a" \
      -DLAPACK_LINKER_FLAGS="-lgfortran -lm"
You can set these values on the command line, with ccmake or by providing an initial cache file, see advanced setup section. Possible manual overrides are explained in detail in the in the config.sample file.

Component selection

The following options control which components of deal.II will be configured, built and installed:

Build configuration

The cmake variable CMAKE_BUILD_TYPE controls the type of build. We support Debug, Release and DebugRelease mode. Default is DebugRelease.

For more information, see the general discussion here.

The build can be further controlled by the following variables:

Selecting a compiler

Compilers can be switched either by command line or by setting CMAKE_(C|CXX|Fortran)_COMPILER:
CC=mpicc CXX=mpicxx FC=mpif90 cmake <...>

cmake -DCMAKE_C_COMPILER="mpicc" -DCMAKE_CXX_COMPILER="mpicxx" -DCMAKE_Fortran_COMPILER="mpif90" <...>
Please note that

deal.II will configure sensible default CXXFLAGS and LDFLAGS depending on platform, compiler and build target. There are two options to override this behaviour:

  1. Override the default configuration by setting the following cached variables:
    DEAL_II_CXX_FLAGS         - used during all builds
    DEAL_II_CXX_FLAGS_DEBUG   - additional flags for the debug library
    DEAL_II_CXX_FLAGS_RELEASE - additional flags for the release library
    
    DEAL_II_LINKER_FLAGS         - used during all builds
    DEAL_II_LINKER_FLAGS_DEBUG   - additional flags for the debug library
    DEAL_II_LINKER_FLAGS_RELEASE - additional flags for the release library
    
    The content of the cached variables will be preserved and added to the end of the default compiler flags, hence providing the possibility for overriding a flag. E.g.: -Wsign-compare, set by the build system, can be overwritten by specifying:
    cmake -DDEAL_II_CXX_FLAGS="-Wno-sign-compare" <...>
    
  2. Set the corresponding environment variables: CFLAGS, CXXFLAGS, or LDFLAGS environment. These variables will also be appended after the default compiler flags (but before the corresponding cached variables).
  3. Disable the configuration completely by adding the flag -D DEAL_II_SETUP_DEFAULT_COMPILER_FLAGS=OFF. Beware of the fact that certain features may still pull in necessary compiler flags.
  4. You can setup additional debug compiler flags to provide test coverage information by adding the flag -D DEAL_II_SETUP_COVERAGE=ON.

Installation

the location, where the deal.II library will be installed when invoking make install to is set with the help of

CMAKE_INSTALL_PREFIX
The default directory structure is:
${CMAKE_INSTALL_PREFIX}/
    bin
    include
    lib${LIB_SUFFIX}
    lib${LIB_SUFFIX}/cmake/deal.II
    share/deal.II/
    share/deal.II/cmake/macros
    ./
    doc
    examples

The default directory structure can be changed by setting the following variables:

DEAL_II_EXECUTABLE_RELDIR
DEAL_II_INCLUDE_RELDIR
DEAL_II_LIBRARY_RELDIR
DEAL_II_PROJECT_CONFIG_RELDIR
DEAL_II_SHARE_RELDIR
DEAL_II_DOCREADME_RELDIR
DEAL_II_DOCHTML_RELDIR
DEAL_II_EXAMPLES_RELDIR

Initial cache file and advanced options

A sample configuration file for preloading the CMake cache with

$ cmake -C config.sample <...>
can be found here. This sample configuration covers all options mentioned in this documentation as well as some advanced aspects in feature configuration.

Compiling only certain parts

While developing the library itself, it is often desirable to only compile certain parts. The build system generated by cmake allows to build specific, selected targets. A common scenario is that you only want to build debug or optimized libraries. This can be achieved using the following commands in the build directory:

make  deal_II.g        # only debug library
make  deal_II          # only release (optimized) library
make  all              # both

make  obj_grid.release # all objects in ./source/grid in release configuration

For a complete list of possible targets that allow even finer-grained control, do

make  help

It is frequently useful to be able to see what a particular command does. In that case, use the following:

make  deal_II.g VERBOSE=ON
This will show, for every command executed, the exact command line with which it was invoked, including compiler arguments, etc. Every command cmake executes starts with a cd command to change the current directory appropriately so that the command line can be copied and executed from anywhere within the build directory.

Note: Just because you can call make deal_II.g to only compile the debug version does not mean that a subsequent make install will only install the debug library. Rather, make install will still want to have both libraries up to date and will therefore invoke make all automatically. To restrict builds in such a way that only one library will be installed, see configuration and installation sections.


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