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Compiling HDF5 Applications

Navigate back: Main / Getting Started with HDF5 / Learning the Basics

# Tools and Instructions on Compiling

Compiling applications to use the HDF5 Library can be as simple as executing:

h5cc -o myprog myprog.c

As an application's file base evolves, there are better solutions using CMake and CMakeLists.txt files. Many tutorials and references can be found with a simple search.

This tutorial section will discuss the use of compile scripts on Linux. See the Using Visual Studio section for compiling with Visual Studio.

# Compile Scripts

When the library is built, the following compile shell scripts are included:

- h5cc: pkg-config based compile shell script for HDF5 C programs
- h5fc: pkg-config based compile shell script for HDF5 F90 programs
- h5c++: pkg-config based compile shell script for HDF5 C++ programs

These scripts are easily used to compile single file applications, such as those included in the tutorial.

Warning | The h5cc/h5fc/h5c++ pkg-config compile scripts are included when building with configure. These versions rely on the pkg-config files in the lib/pkgconfig.

#### Examples of Using the Unix Compile Scripts:

Following are examples of compiling and running an application with the Unix compile scripts:

h5fc myprog.f90
./a.out
h5cc -o myprog myprog.c
./myprog

To see how the libraries linked in with a compile script were configured and built, use the -showconfig option. For example, if using h5cc type:

h5cc -showconfig

#### Detailed Description of Unix Compile Scripts:

The h5cc, h5c++, and h5fc pkg-config compile scripts come with the HDF5 binary distributions (include files, libraries, and utilities) for the platforms we support. The h5c++ and h5fc utilities are ONLY present if the library was built with C++ and Fortran.

#### USING_HDF5_CMake.txt:

    ************************************************************************
    * 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.

           NOTES:
             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.txt for more information.

             3. See https://cmake.org/cmake/help/latest/command/find_package.html
                for more information on the CMake "Config Mode Search Procedure".

    ========================================================================
    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. Created separate source and build directories.
          (CMake commands are executed in the build directory)

       5. Created 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> is:
                * 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 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  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. 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)

    set (LIB_TYPE STATIC) # or SHARED
    string(TOLOWER ${LIB_TYPE} SEARCH_TYPE)

    find_package (HDF5 NAMES hdf5 COMPONENTS C ${SEARCH_TYPE})
    # find_package (HDF5) # Find non-cmake built HDF5
    set_directory_properties(PROPERTIES INCLUDE_DIRECTORIES "${HDF5_INCLUDE_DIR}")
    set (LINK_LIBS ${LINK_LIBS} ${HDF5_C_${LIB_TYPE}_LIBRARY})

    set (example hdf_example)

    add_executable (${example} ${PROJECT_SOURCE_DIR}/${example}.c)
    target_link_libraries (${example} ${LINK_LIBS})

    enable_testing ()
    include (CTest)

    add_test (NAME test_example COMMAND ${example})
    ##########################################################

    ========================================================================
    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:
        https://github.com/HDFGroup/hdf5/blob/develop/release_docs/USING_CMake_Examples.txt

               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
    ========================================================================

# Using Visual Studio

1. If you are building on 64-bit Windows, find the "Platform" dropdown and select "x64". Also select the correct Configuration (Debug, Release, RelWithDebInfo, etc)

2. Set up path for external headers

   The HDF5 install path settings will need to be in the project property sheets per project. Go to "Project" and select "Properties", find "Configuration Properties", and then "C/C++".

   2.1 Add the header path to the "Additional Include Directories" setting. Under "C/C++" find "General" and select "Additional Include Directories". Select "Edit" from the dropdown and add the HDF5 install/include path to the list. (Ex: "C:\Program Files\HDF_Group\HDF5\1.10.9\include")

   2.2 Building applications with the dynamic/shared hdf5 libraries requires that the "H5_BUILT_AS_DYNAMIC_LIB" compile definition be used. Under "C/C++" find "Preprocessor" and select "Preprocessor Definitions". Select "Edit" from the dropdown and add "H5_BUILT_AS_DYNAMIC_LIB" to the list.

3. Set up path for external libraries

   The HDF5 install path/lib settings will need to be in the project property sheets per project. Go to "Project" and select "Properties", find "Configuration Properties", and then "Linker".

   3.1 Add the libraries to the "Additional Dependencies" setting. Under "Linker" find "Input" and select "Additional Dependencies". Select "Edit" from the dropdown and add the required HDF5 install/lib path to the list. (Ex: "C:\Program Files\HDF_Group\HDF5\1.10.9\lib\hdf5.lib")

   3.2 For static builds, the external libraries should be added. For example, to compile a C++ application, enter: libhdf5_cpp.lib libhdf5.lib libz.lib libszaec.lib libaec.lib

# HDF5 Libraries

Following are the libraries included with HDF5. Whether you are using the Unix compile scripts or Makefiles, or are compiling on Windows, these libraries are or may need to be specified. The order they are specified is important on Linux:

HDF5 Static Libraries
Library | Linux Name | Mac Name | Windows Name
--- | --- | --- | ---
HDF5 High Level C++ APIs HDF5 C++ Library HDF5 High Level Fortran APIs HDF5 Fortran Library HDF5 High Level C APIs HDF5 C Library | libhdf5_hl_cpp.a libhdf5_cpp.a libhdf5_hl_fortran.a libhdf5_fortran.a libhdf5_hl.a libhdf5.a | libhdf5_hl_cpp.a libhdf5_cpp.a libhdf5_hl_fortran.a libhdf5_fortran.a libhdf5_hl.a libhdf5.a | Windows libhdf5_hl_cpp.lib libhdf5_cpp.lib libhdf5_hl_fortran.lib libhdf5_fortran.lib libhdf5_hl.lib libhdf5.lib

HDF5 Shared Libraries
Library | Linux Name | Mac Name | Windows Name
--- | --- | --- | ---
HDF5 High Level C++ APIs HDF5 C++ Library HDF5 High Level Fortran APIs HDF5 Fortran Library HDF5 High Level C APIs HDF5 C Library | libhdf5_hl_cpp.so libhdf5_cpp.so libhdf5_hl_fortran.so libhdf5_fortran.so libhdf5_hl.so libhdf5.so | libhdf5_hl_cpp.dylib libhdf5_cpp.dylib libhdf5_hl_fortran.dylib libhdf5_fortran.dylib libhdf5_hl.dylib libhdf5.dylib | hdf5_hl_cpp.lib hdf5_cpp.lib hdf5_hl_fortran.lib hdf5_fortran.lib hdf5_hl.lib hdf5.lib hdf5 Definition HDF5.F90:26

External Libraries
Library | Linux Name | Mac Name | Windows Name
--- | --- | --- | ---
SZIP Compression Library SZIP Compression Library ZLIB or DEFLATE Compression Library | libszaec.a libaec.a libz.a | libszaec.a libaec.a libz.a | libszaec.lib libaec.lib libz.lib

The pre-compiled binaries, in particular, are built (if at all possible) with these libraries as well as with SZIP and ZLIB. If using shared libraries you may need to add the path to the library to LD_LIBRARY_PATH on Linux or on WINDOWS you may need to add the path to the bin folder to PATH.

# Compiling an Application with CMake

## CMake Scripts for Building Applications

See Using CMake to Build Applications to build applications with different languages and options.

For a more complete script (and to help resolve issues) see the script provided with the HDF5 Examples project.

## HDF5 Examples

The installed HDF5 can be verified by compiling the HDF5 Examples project, included with the CMake built HDF5 binaries in the share folder or you can go to the HDF5 Examples in the HDF5 github repository.

Go into the share directory and follow the instructions in Using CMake to Build Examples to build the examples.

In general, users must first set the HDF5_ROOT environment variable to the installed location of the CMake configuration files for HDF5.

For example, on Windows the following path might be set:

HDF5_ROOT=C:/Program Files/HDF_Group/HDF5/z.y.x

For example, on Linux the following path might be set:

HDF5_ROOT=<install root folder>/HDF_Group/HDF5/z.y.x/

## Troubleshooting CMake

#### How do you use find_package with HDF5?

To use find_package you will first need to make sure that HDF5_ROOT is set correctly. For setting this environment variable see the Preconditions in the USING_HDF5_CMake.txt file in the share directory.

See the CMakeLists.txt file provided with these examples for how to use find_package with HDF5.

Please note that the find_package invocation changed to require "shared" or "static":

FIND_PACKAGE(HDF5 COMPONENTS C HL NO_MODULE REQUIRED shared)
FIND_PACKAGE(HDF5 COMPONENTS C HL NO_MODULE REQUIRED static)

Previously, the find_package invocation was:

FIND_PACKAGE(HDF5 COMPONENTS C HL NO_MODULE REQUIRED)

#### My platform/compiler is not included. Can I still use the configuration files?

Yes, you can but you will have to edit the HDF5_Examples.cmake file and update the variable:

CTEST_CMAKE_GENERATOR

The generators for your platform can be seen by typing:

cmake --help
help
void help(char *)

#### What do I do if the build fails?

I received an error during the build and the application binary is not in the build directory as I expected. How do I determine what the problem is?

If the error is not clear, then the first thing you may want to do is replace the -V (Dash Uppercase Vee) option for ctest in the build script to -VV (Dash Uppercase Vee Uppercase Vee). Then remove the build directory and re-run the build script. The output should be more verbose.

If the error is still not clear, then check the log files. You will find those in the build directory. For example, on Unix the log files will be in:

build/Testing/Temporary/

There are log files for the configure, test, and build.

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