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Build and Install HDF5 Applications with CMake

Notes: This short instruction is written for users who want to quickly build HDF5 applications using the CMake tools. Users can adapt these instructions for their own applications. For more information, see the "Minimum C Project Files for CMake" section.

More information about using CMake can be found at the Kitware site, www.cmake.org.

CMake uses the command line; however, the visual CMake tool is available for the configuration step. The steps are similar for all of the operating systems supported by CMake.

  1. CMake for HDF5 development should be usable on any system where CMake is supported. Please send us any comments on how CMake support can be improved on any system.
  2. See the appendix at the bottom of this file for an example of using a ctest script for building and testing. See INSTALL_CMake.md for more information.
  3. See the CMake Config Mode Search Procedure for more information on finding packages.

Table of Contents

I. Preconditions

  1. We suggest you obtain the latest CMake for your platform from the Kitware web site. The HDF5 z.y.x product requires a minimum CMake version of 3.26.

  2. You have installed the HDF5 library built with CMake, by executing the HDF Install Utility (the *.msi file in the binary package for Windows or the *.sh on Linux). You can obtain pre-built binaries from The HDF Group's website at www.hdfgroup.org.

  3. Set the HDF5_ROOT CMake variable (-DHDF5_ROOT=<install_path>) or environment variable (set(ENV{HDF5_ROOT} "<install_path>")) to the installed location of HDF5.

    • On Windows: 
      HDF5_ROOT=C:/Program Files/HDF_Group/HDF5/z.y.x/
    • On Unix: 
      HDF5_ROOT=<install root folder>/HDF_Group/HDF5/z.y.x/

    If you are using shared libraries, you may need to add to the path environment variable. Set the path environment variable to the installed location of the library files for HDF5.

    • On Windows (*.dll): 
      PATH=%PATH%;C:/Program Files/HDF_Group/HDF5/z.y.x/bin
    • On Unix (*.so): 
      LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<install root folder>/HDF_Group/HDF5/z.y.x/lib

    If you are using filter plugin libraries, you will need to set the HDF5_PLUGIN_PATH environment variable.

    • On Windows: 
      HDF5_PLUGIN_PATH=C:/Program Files/HDF_Group/HDF5/z.y.x/lib/plugin
    • On Unix: 
      HDF5_PLUGIN_PATH=<install root folder>/HDF_Group/HDF5/z.y.x/lib/plugin

    (Note: there are no quote characters used on Windows and all platforms use forward slashes).

  4. Create separate source and build directories. (CMake commands are executed in the build directory).

  5. Create a CMakeLists.txt file(s) for your source. See Section III below.

II. Building HDF5 Applications with CMake

Go through these steps to build HDF5 applications with CMake. (The application must support building with CMake.)

  1. Run CMake
  2. Configure the cache settings
  3. Build HDF5 Applications
  4. Test HDF5 Applications

These steps are described in more detail below.

1. Run CMake

The visual CMake executable is named cmake-gui.exe on Windows and should be available in your Start menu. For Linux, UNIX, and Mac users the executable is named cmake-gui and can be found where CMake was installed.

Specify the source and build directories. Make the build and source directories different. For example on Windows, if the source is at c:\MyHDFstuff\hdf5, then use c:\MyHDFstuff\hdf5\build or c:\MyHDFstuff\build\hdf5 for the build directory.

PREFERRED: Users can perform the configuration step without using the visual cmake-gui program. The following is an example command line configuration step executed within the build directory:

cmake -G "<generator>" [-D<options>] <sourcepath>

Where <generator> is (examples):

  • MinGW Makefiles
  • NMake Makefiles
  • Unix Makefiles
  • Visual Studio 15 2017
  • Visual Studio 15 2017 Win64
  • Visual Studio 16 2019 (in addition VS2019 will need to set the -A option, [Win32, x64, ARM, ARM64])
  • Visual Studio 17 2022 (in addition VS2022 will need to set the -A option, [Win32, x64, ARM, ARM64])

<options> can include:

  • BUILD_TESTING:BOOL=ON
  • BUILD_SHARED_LIBS:BOOL=[ON | OFF]

2. Configure the cache settings

2.1 Visual CMake users Click the Configure button. If this is the first time you are running cmake-gui in this directory, you will be prompted for the generator you wish to use (for example on Windows, Visual Studio 16 2019). CMake will read in the CMakeLists.txt files from the source directory and display options for the HDF5 project. After the first configure you can adjust the cache settings and/or specify locations of other programs.

Any conflicts or new values will be highlighted by the configure process in red. Once you are happy with all the settings and there are no more values in red, click the Generate button to produce the appropriate build files.

  • On Windows, if you are using a Visual Studio generator, the solution and project files will be created in the build folder.
  • On linux, if you are using the Unix Makefiles generator, the Makefiles will be created in the build folder.

2.2 Alternative command line example On Windows in the c:\MyHDFstuff\hdf5\build directory:

cmake -G "Visual Studio 16 2019" -A "x64" -DBUILD_TESTING:BOOL=ON ..

3. Build HDF5 Applications

On Windows, you can build HDF5 applications using either the Visual Studio Environment or the command line. The command line is normally used on Linux, Unix, and Mac.

To build from the command line, navigate to your build directory and execute the following:

cmake --build . --config {Debug | Release}

NOTE: --config {Debug | Release} may be optional on your platform. We recommend choosing either Debug or Release on Windows. If you are using the pre-built binaries from HDF, use Release.

3.1 Visual Studio Environment If you wish to use the Visual Studio environment, open the solution file in your build directory. Be sure to select either Debug or Release and build the solution.

4. Test HDF5 Applications

To test the build, navigate to your build directory and execute:

ctest . -C {Debug | Release}

NOTE: -C {Debug | Release} may be optional on your platform. We recommend choosing either Debug or Release to match the build step on Windows.

5. CMake Support Files

The files that support building with CMake are all of the files in the config/cmake folder, the CMakeLists.txt files in each source folder, and CTestConfig.cmake.

  • CTestConfig.cmake is specific to the internal testing performed by The HDF Group. It should be altered for the user's installation and needs.
  • The cacheinit.cmake file settings are used by The HDF Group for daily testing. It should be altered/ignored for the user's installation and needs.

III. Minimum C Project Files for CMake

Given the preconditions in Section I, create a CMakeLists.txt file at the source root. Include the following text in the file:

cmake_minimum_required (VERSION 3.26)
project (HDF5MyApp C)

find_package (HDF5 NAMES hdf5 CONFIG REQUIRED COMPONENTS C)
# find_package (HDF5) # Find non-cmake built HDF5

set (example hdf_example)

add_executable (${example} ${PROJECT_SOURCE_DIR}/${example}.c)
target_link_libraries (${example} PRIVATE hdf5::hdf5)

enable_testing ()
include (CTest)

add_test (NAME test_example COMMAND ${example})

hdf5::hdf5 carries HDF5's include directories and its own dependencies, so there is no need to set INCLUDE_DIRECTORIES or to name the library variables directly.

Public target names

Link against these rather than against hdf5-shared or hdf5-static. The names do not encode the linkage, so the same project file works against a static installation, a shared one, or one providing both:

Target Library
hdf5::hdf5 C
hdf5::hdf5_hl High-level C
hdf5::hdf5_cpp C++
hdf5::hdf5_hl_cpp High-level C++
hdf5::hdf5_fortran Fortran
hdf5::hdf5_hl_fortran High-level Fortran

Each installed tool is available as hdf5::<tool>, for example hdf5::h5diff.

These are the same names CMake's own FindHDF5 module provides, so a project using them does not need to know whether HDF5 was located through FindHDF5 or through HDF5's hdf5-config.cmake. FindHDF5's HDF5::HDF5 aggregate is not defined by hdf5-config.cmake and is only available through FindHDF5.

Choosing static or shared

When an installation provides both, find_package() resolves to the shared libraries and falls back to static. To choose deliberately, request the linkage as a component:

find_package (HDF5 NAMES hdf5 CONFIG REQUIRED COMPONENTS C static)
target_link_libraries (${example} PRIVATE hdf5::hdf5)

Setting HDF5_USE_STATIC_LIBRARIES before find_package() has the same effect, matching FindHDF5. The static and shared components are mutually exclusive; requesting both makes find_package() fail.

The hdf5:: targets follow whichever linkage find_package() resolves, as do the HDF5_<lang>_<LINKAGE>_LIBRARY variables and the Fortran module directory. Before HDF5 2.3.0, a call that named no linkage component preferred the static libraries. A project that relied on that should request the static component or set HDF5_USE_STATIC_LIBRARIES.

Deprecated names

The linkage-qualified targets, and the library variables that go with them, are deprecated as of 2.3.0:

Deprecated Use instead
hdf5-shared, hdf5-static hdf5::hdf5
hdf5_hl-shared, hdf5_hl-static hdf5::hdf5_hl
hdf5_cpp-shared, hdf5_cpp-static hdf5::hdf5_cpp
hdf5_hl_cpp-shared, hdf5_hl_cpp-static hdf5::hdf5_hl_cpp
hdf5_fortran-shared, hdf5_fortran-static hdf5::hdf5_fortran
hdf5_hl_fortran-shared, hdf5_hl_fortran-static hdf5::hdf5_hl_fortran
HDF5_<lang>_SHARED_LIBRARY, HDF5_<lang>_STATIC_LIBRARY the matching hdf5:: target

They will be removed in a future major release, so new projects should use the hdf5:: names, and existing projects should migrate to the new names.

IV. APPENDIX

Below is an example of a ctest script that can be used to build the examples. Adjust the values as necessary. Note that the defaults can be entered on the command line and the build folder is created as a sub-folder. Windows should adjust the forward slash to double backslashes, except for the HDF_DIR environment variable.

NOTE: this file is available in the HDF5 repository, for more information see: USING_CMake_Examples.md

ctest -S HDF5_Examples.cmake -C Release -V -O test.log

Also available at the HDF web site is a CMake application framework template. You can quickly add files to the framework and execute the script to compile your application with an installed HDF5 binary.

For further assistance, send email to help@hdfgroup.org