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HDF5 2.0.0.258fa78
API Reference
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HDF5 2.0.0.258fa78
API Reference
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Navigate back: Main / Getting Started with HDF5 / Learning the Basics
Compiling applications to use the HDF5 Library can be as simple as executing:
As an application's file base evolves, there are better solutions using autotools and makefiles or 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.
When the library is built, the following compile scripts are included:
These scripts are easily used to compile single file applications, such as those included in the tutorial.
| Warning | The h5cc/h5fc/h5c++ compile scripts are included when building with configure. Versions of these compile scripts have also been added to CMake for Linux ONLY. The CMake versions rely on pkgconfig files. |
|---|
Following are examples of compiling and running an application with the Unix compile scripts:
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:
The h5cc, h5c++, and h5fc 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.
************************************************************************
* 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. Using CMake for building and using HDF5 is under active
development. While we have attempted to provide error-free
files, please understand that development with CMake has not
been extensively tested outside of HDF. The CMake specific
files may change before the next release.
2. 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.
3. 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.
4. 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 2.0.x product requires a minimum CMake version
of 3.18. If you are using VS2022, the minimum CMake version is 3.21.
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/HDF5/2.0.x/
On unix:
HDF5_ROOT=<install root folder>/HDF_Group/HDF5/2.0.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/HDF5/2.0.x/bin
On unix (*.so):
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<install root folder>/HDF_Group/HDF5/2.0.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/HDF5/2.0.x/lib/plugin
On unix:
HDF5_PLUGIN_PATH=<install root folder>/HDF_Group/HDF5/2.0.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
* 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 3.18)
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
========================================================================
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.
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
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:
| 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
|
| 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
|
| 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.
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.
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:
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":
Previously, the find_package invocation was:
Yes, you can but you will have to edit the HDF5_Examples.cmake file and update the variable:
The generators for your platform can be seen by typing:
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:
There are log files for the configure, test, and build.
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