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************************************************************************
* Build and Install HDF5 C, C++, Fortran and High-Level Libraries *
* and tools with CMake *
************************************************************************
Table of Contents
Section I: Preconditions
Section II: RECOMMENDED: Quick Start with CMake Presets
Section III: Advanced: Building HDF5 Libraries with CMake Script Mode
Section IV: Advanced: Building HDF5 Libraries with CMake Command Mode
Section V: Further Considerations
Section VI: Options for building HDF5 Libraries with CMake Command Line
Section VII: CMake Option Defaults for HDF5
Section VIII: User Defined Options for HDF5 Libraries with CMake
Section IX: User Defined Compile Flags for HDF5 Libraries with CMake
Section X: Considerations for Cross-Compiling
Section XI: Creating Custom Preset Configurations
Section XII: Using the Library
Section XIII: Using CMake Regex Options for Testing
Section XIV: Java FFM Testing
************************************************************************
========================================================================
I. Preconditions
========================================================================
Obtaining HDF5 source code
1. Create a directory for your development; for example, "myhdfstuff".
2. Obtain HDF5 source from Github
development branch: https://github.com/HDFGroup/hdf5
last release: https://github.com/HDFGroup/hdf5/releases/latest
hdf5-2_"X"_"Y".tar.gz or hdf5-2_"X"_"Y".zip
and put it in "myhdfstuff".
Uncompress the file. There should be a hdf5-2."X"."Y" folder.
3. Obtain HDF5 plugin source from Github
development branch: https://github.com/HDFGroup/hdf5_plugins
Or let the CMake build process download the plugins for you with
the following options:
HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="GIT"(or "TGZ")
HDF5_ENABLE_PLUGIN_SUPPORT:BOOL=ON
CMake version
1. We suggest you obtain the latest CMake from the Kitware web site.
The HDF5 2."X"."Y" product requires a minimum CMake version 3.26.
Note:
To change the install prefix from the platform defaults initialize
the CMake variable, CMAKE_INSTALL_PREFIX. Users of build scripts
will use the INSTALLDIR option.
Note:
See the CMake documentation for more information on setting the
logging levels:
https://cmake.org/cmake/help/latest/variable/CMAKE_MESSAGE_LOG_LEVEL.html
========================================================================
II. RECOMMENDED: Quick Start with CMake Presets
========================================================================
⭐ This is the RECOMMENDED method for building HDF5 2.0 and later.
Prerequisites
-------------
- CMake 3.26 or later (required for HDF5 2.0)
- Ninja build system (recommended, should be downloaded if not available)
- Compiler: GCC, MSVC, or Clang
Quick Start (3 steps)
---------------------
1. Change to the HDF5 source directory:
cd /path/to/hdf5-2.x.y
2. Execute a workflow preset:
cmake --workflow --preset ci-StdShar-GNUC --fresh # Linux/Mac with GCC
cmake --workflow --preset ci-StdShar-MSVC --fresh # Windows with MSVC
cmake --workflow --preset ci-StdShar-Clang --fresh # Linux/Mac with Clang
3. Find your build artifacts in:
../build/ci-StdShar-<compiler>/
That's it! The workflow preset automatically:
- Configures the build
- Compiles libraries and tools
- Runs tests
- Creates installation packages
Available Presets
-----------------
View all available presets:
cmake --list-presets
Common presets:
Standard Builds:
ci-StdShar-GNUC Standard shared libraries (GCC)
ci-StdShar-MSVC Standard shared libraries (MSVC)
ci-StdShar-Clang Standard shared libraries (Clang)
ci-MinShar-GNUC Minimal shared libraries (GCC)
Java Builds:
ci-StdShar-GNUC-Java-FFM Java FFM bindings (GCC)
ci-StdShar-GNUC-Java-JNI Java JNI bindings (GCC)
Maven Deployment (JNI default - Java 8+):
ci-MinShar-GNUC-Maven-Snapshot JNI snapshots for Maven
ci-MinShar-GNUC-Maven JNI release for Maven
Maven Deployment (FFM optional - Java 25+):
ci-MinShar-GNUC-Maven-FFM-Snapshot FFM snapshots for Maven
ci-MinShar-GNUC-Maven-FFM FFM release for Maven
Note: For ROS3 (S3 support), add -DHDF5_ENABLE_ROS3_VFD=ON to any preset
See Section XI for creating custom preset configurations.
Why Use Presets?
----------------
✅ Simpler - No external files to download
✅ Faster - Optimized settings included
✅ Consistent - Same settings across platforms
✅ Modern - CMake 3.26 best practices
✅ Flexible - Easy to customize via CMakeUserPresets.json
Individual Preset Commands (Advanced)
--------------------------------------
If you prefer to run preset steps individually (where <compiler-type> is GNUC, MSVC, or Clang):
cd /path/to/hdf5-source
cmake --preset ci-StdShar-<compiler-type> # Configure
cmake --build --preset ci-StdShar-<compiler-type> # Build
ctest --preset ci-StdShar-<compiler-type> # Test
cpack --preset ci-StdShar-<compiler-type> # Package
The workflow preset (shown in Quick Start above) runs all these steps automatically.
Advanced Build Methods
---------------------
If you cannot use presets or need more control, see:
- Section III: Building with CMake Script Mode (requires external files, for automation/CI)
- Section IV: Building with CMake Command Mode (manual configuration, for advanced users)
========================================================================
III. Advanced: Building HDF5 Libraries with CMake Script Mode
========================================================================
NOTE: Most users should use Section II (CMake Presets) instead.
This method is provided for advanced users and automated builds.
This short set of instructions is written for users who want to quickly
build the HDF5 C, C++ and Fortran shared libraries and tools
from the HDF5 source code package using the CMake tools. This procedure
will use the default settings in the config/cmake/cacheinit.cmake file.
The HDF Group recommends using the presets process to build HDF5.
NOTE: When using the presets process, the CMakePresets.json file in the source
directory will configure, build, test, and package HDF5 with the same options
that are set in the cacheinit.cmake file.
In addition, it will get the optional files listed below that are needed, from
the appropriate repositories.
See Section II: RECOMMENDED Quick Start with CMake Presets
-------------------------------------------------------------------------
-------------------------------------------------------------------------
Individual files needed as mentioned in this document
-------------------------------------------------------------------------
Download from https://github.com/HDFGroup/hdf5/blob/develop/config/cmake/scripts:
CTestScript.cmake -- CMake build script
HDF5config.cmake -- CMake configuration script
HDF5options.cmake -- CMake configuration options script
External compression plugin libraries from https://github.com/HDFGroup/hdf5_plugins:
hdf5_plugins.tar.gz
External compression szip and zlib libraries:
ZLIB "https://github.com/madler/zlib/releases/download/v1.3.1/zlib-1.3.1.tar.gz"
ZLIBNG "https://github.com/zlib-ng/zlib-ng/archive/refs/tags/2.2.4.tar.gz"
LIBAEC "https://github.com/MathisRosenhauer/libaec/releases/download/v1.1.3/libaec-1.1.3.tar.gz"
-------------------------------------------------------------------------
-------------------------------------------------------------------------
Build scripts for windows or linux
-----------------------------------------------
To build HDF5 with the SZIP and ZLIB external libraries you will need to:
1. Change to the development directory "myhdfstuff".
2. Download/copy the individual files mentioned above to "myhdfstuff".
Do not uncompress the tar.gz files.
3. Change to the source directory "hdf5-2.x.y".
CTestScript.cmake file should not be modified.
4. Edit the platform configuration file, HDF5options.cmake, if you want to change
the default build environment. The file is a compilation of the most used
options and by commenting/uncommenting lines the options can easily be changed.
5. From the "myhdfstuff" directory execute the CTest Script with the
following options:
On 32-bit Windows with Visual Studio 2022, execute:
ctest -S HDF5config.cmake,BUILD_GENERATOR=VS2022 -C Release -VV -O hdf5.log
On 64-bit Windows with Visual Studio 2022, execute:
ctest -S HDF5config.cmake,BUILD_GENERATOR=VS202264 -C Release -VV -O hdf5.log
On 32-bit Windows with Visual Studio 2019, execute:
ctest -S HDF5config.cmake,BUILD_GENERATOR=VS2019 -C Release -VV -O hdf5.log
On 64-bit Windows with Visual Studio 2019, execute:
ctest -S HDF5config.cmake,BUILD_GENERATOR=VS201964 -C Release -VV -O hdf5.log
On 32-bit Windows with Visual Studio 2017, execute:
ctest -S HDF5config.cmake,BUILD_GENERATOR=VS2017 -C Release -VV -O hdf5.log
On 64-bit Windows with Visual Studio 2017, execute:
ctest -S HDF5config.cmake,BUILD_GENERATOR=VS201764 -C Release -VV -O hdf5.log
On Linux and Mac, execute:
ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix -C Release -VV -O hdf5.log
The supplied build scripts are versions of the above.
The command above will configure, build, test, and create an install
package in the myhdfstuff folder. It will have the format:
HDF5-2.X.Y-<platform>.<zip or tar.gz>
On Unix, <platform> will be "Linux". A similar .sh file will also be created.
On Windows, <platform> will be "win64" or "win32". If you have an
installer on your system, you will also see a similar file that ends
in either .exe (NSIS) or .msi (WiX).
Notes on the command line options.
The -S option uses the script version of ctest.
The value for the -C option (as shown above, "-C Release") must
match the setting for CTEST_CONFIGURATION_TYPE in the platform
configuration file.
The -VV option is for most verbose; use -V for less verbose.
The "-O hdf5.log" option saves the output to a log file hdf5.log.
6. To install, "X" is the current release version
On Windows (with WiX installed), execute:
HDF5-2."X"."Y"-win32.msi or HDF5-2."X"."Y"-win64.msi
By default this program will install the hdf5 library into the
"C:\Program Files" directory and will create the following
directory structure:
HDF_Group
--HDF5
----2."X"."Y"
------bin
------include
------lib
--------plugin
------cmake
On Linux, change to the install destination directory
(create it if doesn't exist) and execute:
<path-to>/myhdfstuff/HDF5-2."X"."Y"-Linux.sh
After accepting the license, the script will prompt:
By default the HDF5 will be installed in:
"<current directory>/HDF5-2."X"."Y"-Linux"
Do you want to include the subdirectory HDF5-2."X"."Y"-Linux?
Saying no will install in: "<current directory>" [Yn]:
Note that the script will create the following directory structure
relative to the install point:
HDF_Group
--HDF5
----2."X"."Y"
------bin
------include
------lib
--------plugin
------share
On Mac you will find HDF5-2."X"."Y"-Darwin.dmg in the myhdfstuff folder. Click
on the dmg file to proceed with installation. After accepting the license,
there will be a folder with the following structure:
HDF_Group
--HDF5
----2."X"."Y"
------bin
------include
------lib
--------plugin
------share
By default the installation will create the bin, include, lib and cmake
folders in the <install destination directory>/HDF_Group/HDF5/2."X"."Y"
The <install destination directory> depends on the build platform;
Windows will set the default to:
C:/Program Files/HDF_Group/HDF5/2."X"."Y"
Linux will set the default to:
"myhdfstuff/HDF_Group/HDF5/2."X"."Y"
The default can be changed by adding ",INSTALLDIR=<my new dir>" to the
"ctest -S HDF5config.cmake..." command. For example on linux:
ctest -S HDF5config.cmake,INSTALLDIR=/usr/local/myhdf5,BUILD_GENERATOR=Unix -C Release -VV -O hdf5.log
========================================================================
IV. Advanced: Building HDF5 Libraries with CMake Command Mode
========================================================================
NOTE: Most users should use Section II (CMake Presets) instead.
This method is provided for advanced users who need manual control.
Notes: This short set of instructions is written for users who want to
quickly build just the HDF5 C static library and tools from
the HDF5 source code package using the CMake command line tools.
Avoid the use of drive letters in paths on Windows.
Go through these steps:
1. Change to the development directory "myhdfstuff".
2. Uncompress the HDF5 source file
3. Create a folder "build" in the "myhdfstuff" directory.
4. Change into the "build" folder.
5. Configure the C library, tools and tests with one of the following commands:
On Windows 32 bit
cmake -G "Visual Studio 16 2019" -A Win32 -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DHDF5_BUILD_TOOLS:BOOL=ON ..\hdf5-2."X"."Y"
On Windows 64 bit
cmake -G "Visual Studio 16 2019" -A x64 -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DHDF5_BUILD_TOOLS:BOOL=ON ..\hdf5-2."X"."Y"
On Linux and Mac
cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DHDF5_BUILD_TOOLS:BOOL=ON ../hdf5-2."X"."Y"
where "X" is the current release version.
6. Build the C library, tools and tests with this command:
cmake --build . --config Release
7. Test the C library and tools with this command:
ctest . -C Release
8. Create an install image with this command:
cpack -C Release CPackConfig.cmake
9. To install
On Windows (with WiX installed), execute:
HDF5-2."X"."Y"-win32.msi or HDF5-2."X"."Y"-win64.msi
By default this program will install the hdf5 library into the
"C:\Program Files" directory and will create the following
directory structure:
HDF_Group
--HDF5
----2."X"."Y"
------bin
------include
------lib
--------plugin
------cmake
On Linux, change to the install destination directory
(create if doesn't exist) and execute:
<path-to>/myhdfstuff/build/HDF5-2."X"."Y"-Linux.sh
After accepting the license, the script will prompt:
By default the HDF5 will be installed in:
"<current directory>/HDF5-2."X"."Y"-Linux"
Do you want to include the subdirectory HDF5-2."X"."Y"-Linux?
Saying no will install in: "<current directory>" [Yn]:
Note that the script will create the following directory structure
relative to the install point:
HDF_Group
--HDF5
----2."X"."Y"
------bin
------include
------lib
--------plugin
------share
On Mac you will find HDF5-2."X"."Y"-Darwin.dmg in the build folder. Click
on the dmg file to proceed with installation. After accepting the license,
there will be a folder with the following structure:
HDF_Group
--HDF5
----2."X"."Y"
------bin
------include
------lib
--------plugin
------share
========================================================================
V. Further Considerations
========================================================================
1. We suggest you obtain the latest CMake from the Kitware
web site. The HDF5 2."X"."Y" product requires a minimum CMake version 3.26.
2. If you plan to use Zlib or Szip (aka libaec):
A. Download the binary packages and install them in a central location.
For example on Windows, create a folder extlibs and install the
packages there. Add the following CMake options:
-DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib
-DZLIB_INCLUDE_DIR:PATH=some_location/include
-DZLIB_USE_EXTERNAL:BOOL=OFF
-DSZIP_LIBRARY:FILEPATH=some_location/lib/libszaec.lib
-DSZIP_INCLUDE_DIR:PATH=some_location/include
-Dlibaec_LIBRARY:FILEPATH=some_location/lib/libaec.lib
-Dlibaec_INCLUDE_DIR:PATH=some_location/include
-DSZIP_USE_EXTERNAL:BOOL=OFF
where "some_location" is the full path to the extlibs folder.
Also if the appropriate environment variable is set, the above options are not required;
set(ENV{ZLIB_ROOT} "some_location")
set(ENV{SZIP_ROOT} "some_location")
set(ENV{libaec_ROOT} "some_location")
Note that if there is a problem finding the libraries, try adding the
CMake variable CMAKE_FIND_DEBUG_MODE:BOOL=ON to the command line.
B. Use source packages from an GIT server by adding the following CMake
options:
HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="GIT"
ZLIB_GIT_URL:STRING="https://some_location/zlib" or ZLIBNG_GIT_URL:STRING="https://some_location/zlibng"
ZLIB_GIT_BRANCH="some_branch" or ZLIBNG_GIT_BRANCH="some_branch"
SZIP_GIT_URL:STRING="https://some_location/szip"
SZIP_GIT_BRANCH="some_branch"
LIBAEC_GIT_URL:STRING="https://some_location/libaec"
LIBAEC_GIT_BRANCH="some_branch"
where "some_location" is the URL to the GIT repository and "some_branch" is
a branch in the repository, usually the default. Also set
CMAKE_BUILD_TYPE to the configuration type.
C. Use source packages from a compressed file by adding the following
CMake options:
HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ"
ZLIB_TGZ_NAME:STRING="zlib_src.ext" or ZLIBNG_TGZ_NAME:STRING="zlibng_src.ext"
LIBAEC_TGZ_NAME:STRING="libaec_src.ext"
TGZPATH:STRING="some_location"
where "some_location" is the URL or full path to the compressed
file and ext is the type of compression file. Also set CMAKE_BUILD_TYPE
to the configuration type during configuration. See the settings in the
config/cmake/cacheinit.cmake file HDF uses for testing.
D. Use original source packages from a compressed file by adding the following
CMake options:
LIBAEC_TGZ_NAME:STRING="szip_src.ext"
LIBAEC_TGZ_ORIGPATH:STRING="some_location"
ZLIB_TGZ_NAME:STRING="zlib_src.ext" or ZLIBNG_TGZ_NAME:STRING="zlibng_src.ext"
ZLIB_TGZ_ORIGPATH:STRING="some_location" or ZLIBNG_TGZ_ORIGPATH:STRING="some_location"
HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ"
where "some_location" is the URL and by setting
ZLIB_USE_LOCALCONTENT:BOOL=OFF
LIBAEC_USE_LOCALCONTENT:BOOL=OFF
or full path to the compressed file and ext is the type of compression file.
Also set CMAKE_BUILD_TYPE to the configuration type during configuration.
See the settings in the config/cmake/cacheinit.cmake file HDF uses for testing.
The files can also be retrieved from a local path if necessary
TGZPATH:STRING="some_location"
by setting
ZLIB_USE_LOCALCONTENT:BOOL=ON
LIBAEC_USE_LOCALCONTENT:BOOL=ON
3. If you plan to use compression plugins:
A. Use source packages from an GIT server by adding the following CMake
options:
HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="GIT"
PLUGIN_GIT_URL:STRING="http://some_location/plugins"
PLUGIN_GIT_BRANCH="some_branch"
where "some_location" is the URL to the GIT repository and "some_branch" is
a branch in the repository, usually the default. Also set
CMAKE_BUILD_TYPE to the configuration type.
B. Use source packages from a compressed file by adding the following
CMake options:
HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ"
PLUGIN_TGZ_NAME:STRING="plugin_src.ext"
TGZPATH:STRING="some_location"
where "some_location" is the URL or full path to the compressed
file and ext is the type of compression file. Also set CMAKE_BUILD_TYPE
to the configuration type during configuration. See the settings in the
config/cmake/cacheinit.cmake file HDF uses for testing.
4. If you are building on Apple Darwin platforms, you should add the
following options:
Compiler choice - use xcode by setting the ENV variables of CC and CXX
Shared fortran is not supported, build static:
BUILD_SHARED_LIBS:BOOL=OFF
Additional options:
CMAKE_ANSI_CFLAGS:STRING=-fPIC
CTEST_USE_LAUNCHERS:BOOL=ON
5. Windows developers should install NSIS or WiX to create an install image with CPack.
Visual Studio Express users will not be able to package HDF5 into
an install image executable.
6. Developers can copy the config/cmake/cacheinit.cmake file and alter the
the settings for the developers' environment. Then the only options needed
on the command line are those options that are different. Example using HDF
default cache file:
cmake -C ../config/cmake/cacheinit.cmake -G "Visual Studio 16 2019" \
-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=OFF \
-DCMAKE_BUILD_TYPE:STRING=Release ..
7. CMake uses a toolchain of utilities to compile, link libraries and
create archives, and other tasks to drive the build. The toolchain
utilities available are determined by the languages enabled. In normal
builds, CMake automatically determines the toolchain for host builds
based on system introspection and defaults. In cross-compiling
scenarios, a toolchain file may be specified with information about
compiler and utility paths.
Variables and Properties
Several variables relate to the language components of a toolchain which
are enabled. CMAKE_<LANG>_COMPILER is the full path to the compiler used
for <LANG>. CMAKE_<LANG>_COMPILER_ID is the identifier used by CMake for
the compiler and CMAKE_<LANG>_COMPILER_VERSION is the version of the compiler.
The CMAKE_<LANG>_FLAGS variables and the configuration-specific equivalents
contain flags that will be added to the compile command when compiling a
file of a particular language.
As the linker is invoked by the compiler driver, CMake needs a way to
determine which compiler to use to invoke the linker. This is calculated
by the LANGUAGE of source files in the target, and in the case of static
libraries, the language of the dependent libraries. The choice CMake makes
may be overridden with the LINKER_LANGUAGE target property.
See the CMake help for more information on using toolchain files.
To use a toolchain file with the supplied cmake scripts, see the
HDF5options.cmake file under the toolchain section.
Notes: CMake and HDF5
1. CMake support 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. Visit the
Kitware site for more information about CMake.
2. Build and test results can be submitted to our HDF5 CDash server:
The CDash server for community submissions of hdf5 is at
https://my.cdash.org.
We ask that all submissions include the configuration information and
contact information in the CTest Notes Files upload step. See the
current reports on CDash for examples.
Please follow the convention that "NIGHTLY" submissions maintain the same
configuration every time. "EXPERIMENTAL" submissions can be expected to
be different for each submission.
3. See the appendix at the bottom of this file for examples of using
a ctest script for building and testing. Using a ctest script is
preferred because of its flexibility.
Notes: CMake in General
1. More information about using CMake can be found at the Kitware site at
www.cmake.org.
2. CMake uses the command line; however, the visual CMake tool is
available for the configuration step. The steps are similar for
all the operating systems supported by CMake.
3. Setting the installation location from the command line at configure time
a. Using the --install-prefix command line option, which is available since
CMake version 3.21:
cmake --install-prefix /my/folder/to/install/to ..
b. Using -DCMAKE_INSTALL_PREFIX :
cmake -DCMAKE_INSTALL_PREFIX=/my/folder/to/install/to ..
c. Using the CMAKE_INSTALL_PREFIX environment variable, which is available
since CMake version 3.29:
CMAKE_INSTALL_PREFIX=/my/folder/to/install/to cmake ..
========================================================================
VI. Options for Building HDF5 Libraries with CMake Command Line
========================================================================
To build the HDF5 Libraries with CMake, go through these five steps:
1. Run CMake
2. Configure the cache settings
3. Build HDF5
4. Test HDF5
5. Package HDF5 (create install image)
These five steps are described in 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.
Another option is to use the presets file, CMakePresets.json, to configure,
build, test, and package HDF5. See section XI: Creating Custom Preset Configurations for
compiling for use of that file. You can create a CMakeUserPresets.json file to create a
specific configuration for your environment. Note that Visual Studio and XCode can
use the presets files.
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 as the
build directory.
RECOMMENDED:
Users can perform the configuration step without using the visual
cmake-gui program. We use the file cacheinit.cmake in the
config/cmake source folder for our testing. This file enables all of the
basic options and we turn specific options on or off for testing
using the following command line within the build directory:
cmake -C <sourcepath>/config/cmake/cacheinit.cmake -G "<generator>" [-D<options>] <sourcepath>
Where <generator> is (examples):
* MinGW Makefiles
* NMake Makefiles
* Unix Makefiles
* Ninja
* Visual Studio 15 2017
* Visual Studio 15 2017 Win64
* Visual Studio 16 2019
* Visual Studio 17 2022
<options> is:
For installed SZIP/libaec:
* SZIP_INCLUDE_DIR:PATH=<path to szip includes directory>
* SZIP_LIBRARY:FILEPATH=<path to szip/library file>
* libaec_INCLUDE_DIR:PATH=<path to libaec includes directory>
* libaec_LIBRARY:FILEPATH=<path to libaec/library file>
or
* SZIP_ROOT:PATH=<path to szip root directory>
* libaec_ROOT:PATH=<path to libaec root directory>
For installed ZLIB/ZLIBNG:
* ZLIB_INCLUDE_DIR:PATH=<path to zlib includes directory>
* ZLIB_LIBRARY:FILEPATH=<path to zlib/library file>
or
* ZLIB_ROOT:PATH=<path to zlib root directory>
* <HDF5OPTION>:BOOL=[ON | OFF]
<cacheinit.cmake> highlights are:
# This is the CMakeCache file used by HDF Group for daily tests.
set (CMAKE_INSTALL_FRAMEWORK_PREFIX "Library/Frameworks" CACHE STRING "Frameworks installation directory" FORCE)
set (HDF_PACKAGE_NAMESPACE "hdf5::" CACHE STRING "Name for HDF package namespace (can be empty)" FORCE)
set (HDF5_BUILD_CPP_LIB ON CACHE BOOL "Build C++ support" FORCE)
set (HDF5_BUILD_FORTRAN ON CACHE BOOL "Build FORTRAN support" FORCE)
set (HDF5_BUILD_JAVA ON CACHE BOOL "Build JAVA support" FORCE)
set (HDF5_ENABLE_ALL_WARNINGS ON CACHE BOOL "Enable all warnings" FORCE)
set (HDF5_ALLOW_EXTERNAL_SUPPORT "TGZ" CACHE STRING "Allow External Library Building (NO GIT TGZ)" FORCE)
########################
# compression options
########################
set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of ZLIB package" FORCE)
set (ZLIB_TGZ_NAME "zlib-1.3.1.tar.gz" CACHE STRING "Use HDF5_ZLib from compressed file" FORCE)
set (ZLIB_TGZ_ORIGPATH "https://github.com/madler/zlib/releases/download/v1.3.1" CACHE STRING "Use ZLIB from original location" FORCE)
set (ZLIB_USE_LOCALCONTENT ON CACHE BOOL "Use local file for ZLIB FetchContent" FORCE)
set (ZLIB_GIT_URL "https://github.com/madler/zlib.git" CACHE STRING "Use ZLIB from GitHub repository" FORCE)
set (ZLIB_GIT_BRANCH "develop" CACHE STRING "" FORCE)
set (HDF5_USE_ZLIB_NG OFF CACHE BOOL "Use zlib-ng library as zlib library" FORCE)
set (ZLIBNG_PACKAGE_NAME "zlib-ng" CACHE STRING "Name of ZLIBNG package" FORCE)
set (ZLIBNG_TGZ_NAME "2.2.4.tar.gz" CACHE STRING "Use HDF5_ZLib from compressed file" FORCE)
set (ZLIBNG_TGZ_ORIGPATH "https://github.com/zlib-ng/zlib-ng/archive/refs/tags" CACHE STRING "Use ZLIBNG from original location" FORCE)
set (ZLIBNG_GIT_URL "https://github.com/zlib-ng/zlib-ng.git" CACHE STRING "Use ZLIBNG from GitHub repository" FORCE)
set (ZLIBNG_GIT_BRANCH "develop" CACHE STRING "" FORCE)
set (LIBAEC_PACKAGE_NAME "libaec" CACHE STRING "Name of AEC SZIP package" FORCE)
set (LIBAEC_TGZ_NAME "libaec-1.1.3.tar.gz" CACHE STRING "Use SZip AEC from compressed file" FORCE)
set (LIBAEC_TGZ_ORIGPATH "https://github.com/MathisRosenhauer/libaec/releases/download/v1.1.3" CACHE STRING "Use LIBAEC from original location" FORCE)
set (LIBAEC_USE_LOCALCONTENT ON CACHE BOOL "Use local file for LIBAEC FetchContent" FORCE)
set (LIBAEC_GIT_URL "https://github.com/MathisRosenhauer/libaec.git" CACHE STRING "Use LIBAEC from GitHub repository" FORCE)
set (LIBAEC_GIT_BRANCH "v1.1.3" CACHE STRING "" FORCE)
########################
# filter plugin options
########################
set (PLUGIN_TGZ_ORIGPATH "https://github.com/HDFGroup/hdf5_plugins/releases/download/snapshot" CACHE STRING "Use PLUGINS from original location" FORCE)
set (PLUGIN_TGZ_NAME "hdf5_plugins-master.tar.gz" CACHE STRING "Use PLUGINS from compressed file" FORCE)
set (PLUGIN_USE_LOCALCONTENT ON CACHE BOOL "Use local file for PLUGIN FetchContent" FORCE)
set (PLUGIN_PACKAGE_NAME "pl" CACHE STRING "Name of PLUGIN package" FORCE)
set (PLUGIN_GIT_URL "https://github.com/HDFGroup/hdf5_plugins.git" CACHE STRING "Use plugins from HDF Group repository" FORCE)
set (PLUGIN_GIT_BRANCH "master" CACHE STRING "" FORCE)
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 14).
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 the 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 Preferred command line example on Windows in c:\MyHDFstuff\hdf5\build directory:
cmake -C ../config/cmake/cacheinit.cmake -G "Visual Studio 16 2019" "-Ax64" \
-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=OFF \
-DCMAKE_BUILD_TYPE:STRING=Release ..
2.3 On Windows, if you are using a Visual Studio Express version you must
be sure that the following two options are correctly set/unset:
HDF5_NO_PACKAGES:BOOL=ON
HDF5_USE_FOLDERS:BOOL=OFF
3. Build HDF5
On Windows, you can build HDF5 using either the Visual Studio Environment
or the command line. The command line can be used on all platforms;
Windows, 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.
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.
3.2.1 The external libraries (zlib, szip and plugins) can be configured
to allow building the libraries by downloading from a GIT repository.
The option is 'HDF5_ALLOW_EXTERNAL_SUPPORT'; by adding the following
configuration option:
-DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="GIT"
The options to control the GIT parameters (config/cmake/cacheinit.cmake file) are:
ZLIB_GIT_URL:STRING="https://${git_url}/zlib"
ZLIB_GIT_BRANCH="${git_branch}"
SZIP_GIT_URL:STRING="https://${git_url}/szip"
SZIP_GIT_BRANCH="${git_branch}"
LIBAEC_GIT_URL:STRING="https://${git_url}/libaec"
LIBAEC_GIT_BRANCH="${git_branch}"
PLUGIN_GIT_URL:STRING="https://${git_url}/plugin"
PLUGIN_GIT_BRANCH="${git_branch}"
${git_url} should be changed to your location and ${git_branch} is
your branch in the repository. Also define CMAKE_BUILD_TYPE
to be the configuration type.
3.2.2 Or the external libraries (zlib, szip and plugins) can be configured
to allow building the libraries by using a compressed file.
The option is 'HDF5_ALLOW_EXTERNAL_SUPPORT' and is enabled by
adding the following configuration option:
-DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ"
The options to control the TGZ URL (config/cmake/cacheinit.cmake
file) are:
ZLIB_TGZ_NAME:STRING="zlib_src.ext"
LIBAEC_TGZ_NAME:STRING="libaec_src.ext"
PLUGIN_TGZ_NAME:STRING="plugin_src.ext"
TGZPATH:STRING="some_location"
where "some_location/xxxx_src.ext" is the URL or full path to
the compressed file and where ext is the type of the compression
file such as .bz2, .tar, .tar.gz, .tgz, or .zip. Also define
CMAKE_BUILD_TYPE to be the configuration type.
NOTE: the file named by LIBAEC_TGZ_NAME is used to build SZIP.
4. Test HDF5
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. Packaging HDF5 (create an install image)
To package the build into a simple installer using WiX toolset or the NullSoft installer NSIS
on Windows, or into compressed files (.tar.gz, .sh, .zip), use the CPack tool.
To package the build, navigate to your build directory and execute;
cpack -C {Debug | Release} CPackConfig.cmake
NOTE: See note 8 of this document for NSIS information.
See note 9 of this document for WiX information.
Also, if you are using a Visual Studio Express version or
want to disable the packaging components, set HDF5_NO_PACKAGES
to ON (on the command line add -DHDF5_NO_PACKAGES:BOOL=ON)
6. The files that support building HDF5 with CMake are all 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.
7. More information about using CMake can be found at the Kitware site,
www.cmake.org.
8. Nullsoft Scriptable Install System
The Nullsoft Scriptable Install System (NSIS) is an open source installation
system. It was created by the WinAmp authors to distribute that application,
but it is now a general-purpose system which anyone might use. NSIS installers
recognize /S for silent installation and /D=dir to specify the
"output directory", which is where the program will be installed. These
options are case-sensitive, so be sure to type them in upper case.
9. WiX Toolset
WiX--the Windows Installer XML toolset--lets developers create installers for
Windows Installer, the Windows installation engine. See http://wixtoolset.org.
10. Backward compatibility
The 2.0.0 version of the HDF5 library can be configured to
set all versioned functions to the version that was available in one of these HDF5_DEFAULT_API_VERSIONs
HDF5_DEFAULT_API_VERSION:STRING=v114
HDF5_DEFAULT_API_VERSION:STRING=v112
HDF5_DEFAULT_API_VERSION:STRING=v110
HDF5_DEFAULT_API_VERSION:STRING=v18
HDF5_DEFAULT_API_VERSION:STRING=v16
This allows existing code to be compiled with the
v2.0 library without requiring immediate changes to the application
source code.
Note that because 2.0.0 is a major release, as long as the existing application
code doesn't use symbols removed in 2.0.0, the code can be compiled and run with
the new library.
For additional configuration options and other details,
see "API Compatibility Macros":
https://support.hdfgroup.org/documentation/hdf5/latest/api-compat-macros.html
11. Building doxygen
One can optionally build the doxygen files for the HDF5 C library.
By default, this option is disabled. To build the html files, specify
'HDF5_BUILD_DOC'.
cmake -G "<generator>" -DHDF5_BUILD_DOC:BOOL=ON <sourcepath>
Configuration will halt if the required applications are not available.
To build:
cmake --build . --config {Debug | Release}
or
make doxygen
12. Parallel versus serial library
The HDF5 library can be configured to use MPI and MPI-IO for
parallelism on a distributed multi-processor system. Read the
file README_HPC.md for detailed information.
HDF5_ENABLE_PARALLEL:BOOL=ON
The threadsafe, C++ and Java interfaces are not compatible
with the parallel option.
Unless HDF5_ALLOW_UNSUPPORTED has been specified on the configure line,
the following options must be disabled:
HDF5_ENABLE_THREADSAFE, HDF5_BUILD_CPP_LIB, HDF5_BUILD_JAVA
13. Threadsafe capability
The HDF5 library can be configured to be thread-safe (on a very
large scale) with the HDF5_ENABLE_THREADSAFE flag to the configure
script. For further information, see the "Technical Notes" category
in the documentation:
https://support.hdfgroup.org/documentation/hdf5/latest/
The high-level, C++, Fortran and Java interfaces are not compatible
with the thread-safety option because the lock is not hoisted
into the higher-level API calls.
Unless HDF5_ALLOW_UNSUPPORTED has been specified on the configure line,
the following options must be disabled:
HDF5_BUILD_HL_LIB, HDF5_BUILD_FORTRAN, HDF5_BUILD_CPP_LIB, HDF5_BUILD_JAVA
========================================================================
VII. CMake Option Defaults for HDF5
========================================================================
In the options listed below, there are three columns of information:
Option Name, Option Description, and Option Default.
The config/cmake/cacheinit.cmake or CMakePresets.json file can override the following values.
---------------- General Build Options -------------------------------------
BUILD_SHARED_LIBS "Build Shared Libraries" ON
BUILD_STATIC_LIBS "Build Static Libraries" ON
BUILD_STATIC_EXECS "Build Static Executables" OFF
BUILD_TESTING "Build HDF5 Unit Testing" ON
if (WINDOWS)
HDF5_DISABLE_PDB_FILES "Do not install PDB files" OFF
---------------- HDF5 Build Options ----------------------------------------
HDF5_BUILD_CPP_LIB "Build HDF5 C++ Library" OFF
HDF5_BUILD_EXAMPLES "Build HDF5 Library Examples" ON
HDF5_BUILD_FORTRAN "Build FORTRAN support" OFF
HDF5_BUILD_JAVA "Build JAVA support" OFF
HDF5_BUILD_HL_LIB "Build HIGH Level HDF5 Library" ON
HDF5_BUILD_TOOLS "Build HDF5 Tools" ON
HDF5_BUILD_PARALLEL_TOOLS "Build Parallel HDF5 Tools" OFF
HDF5_BUILD_STATIC_TOOLS "Build Static Tools Not Shared Tools" OFF
----------------- HDF5 Maven Integration Options ----------------------------
HDF5_ENABLE_MAVEN_DEPLOY "Enable Maven repository deployment" OFF
HDF5_MAVEN_SNAPSHOT "Build Maven snapshot versions" OFF
HDF5_ENABLE_JNI "Force JNI implementation (default: auto-detect)" ON
Java Implementation Selection (as of HDF5 2.0):
HDF5 Java bindings support two native interface implementations:
- JNI (Java Native Interface): Default, works with Java 8+, production-stable
- FFM (Foreign Function & Memory): Optional, requires Java 25+, modern native access
Maven Artifacts:
- org.hdfgroup:hdf5-java-ffm - FFM implementation
- org.hdfgroup:hdf5-java-jni - JNI implementation
Both implementations use the same hdf.hdf5lib.* package structure for seamless migration.
To build HDF5 with Maven deployment support:
cmake -DHDF5_BUILD_JAVA:BOOL=ON -DHDF5_ENABLE_MAVEN_DEPLOY:BOOL=ON ../hdf5
To build Maven snapshot versions for development:
cmake -DHDF5_BUILD_JAVA:BOOL=ON -DHDF5_ENABLE_MAVEN_DEPLOY:BOOL=ON -DHDF5_MAVEN_SNAPSHOT:BOOL=ON ../hdf5
Note: FFM is selected for Java 25+ if HDF5_ENABLE_JNI is OFF, JNI for older versions.
To force JNI even with Java 25+:
cmake -DHDF5_BUILD_JAVA:BOOL=ON -DHDF5_ENABLE_MAVEN_DEPLOY:BOOL=ON -DHDF5_ENABLE_JNI:BOOL=ON ../hdf5
Or use the Maven-enabled CMake presets (recommended):
# Minimal build for Java artifacts only (recommended for Maven deployment)
# Linux (GCC) - JNI (default, Java 8+):
cmake --workflow --preset ci-MinShar-GNUC-Maven --fresh # JNI Release
cmake --workflow --preset ci-MinShar-GNUC-Maven-Snapshot --fresh # JNI Snapshot
# Linux (GCC) - FFM (optional, Java 25+):
cmake --workflow --preset ci-MinShar-GNUC-Maven-FFM --fresh # FFM Release
cmake --workflow --preset ci-MinShar-GNUC-Maven-FFM-Snapshot --fresh # FFM Snapshot
# Windows (MSVC) - JNI (default):
cmake --workflow --preset ci-MinShar-MSVC-Maven --fresh # JNI Release
cmake --workflow --preset ci-MinShar-MSVC-Maven-Snapshot --fresh # JNI Snapshot
# Windows (MSVC) - FFM (optional):
cmake --workflow --preset ci-MinShar-MSVC-Maven-FFM --fresh # FFM Release
cmake --workflow --preset ci-MinShar-MSVC-Maven-FFM-Snapshot --fresh # FFM Snapshot
# macOS (Clang) - JNI (default):
cmake --workflow --preset ci-MinShar-Clang-Maven --fresh # JNI Release
cmake --workflow --preset ci-MinShar-Clang-Maven-Snapshot --fresh # JNI Snapshot
# macOS (Clang) - FFM (optional):
cmake --workflow --preset ci-MinShar-Clang-Maven-FFM --fresh # FFM Release
cmake --workflow --preset ci-MinShar-Clang-Maven-FFM-Snapshot --fresh # FFM Snapshot
# ROS3 VFD (S3 cloud storage) - Add to any preset above:
cmake --workflow --preset ci-MinShar-GNUC-Maven --fresh -DHDF5_ENABLE_ROS3_VFD=ON
Note: Presets are platform-specific. Use 'cmake --list-presets' to see
available presets for your current platform.
Note: Minimal Maven presets skip examples, testing, tools, C++, and Fortran
builds to optimize for Java artifact generation only.
Java Examples Maven Integration:
The HDF5 Java examples are available as a separate Maven artifact:
- org.hdfgroup:hdf5-java-examples
- Platform-specific dependencies ensure compatibility with HDF5 Java library
- Complete examples with documentation for all HDF5 Java functionality
- See HDF5Examples/JAVA/README-MAVEN.md for usage instructions
Testing Java Examples with Maven Artifacts:
- Maven staging workflow validates examples against artifacts
- Cross-platform testing ensures compatibility on all supported platforms
- Native library error handling validates JAR structure in Maven-only environments
- Fork-based testing allows validation on repository forks before canonical deployment
- Dynamic repository workflows adapt to any GitHub repository automatically
---------------- HDF5 Folder Build Options ---------------------------------
Defaults relative to $<INSTALL_PREFIX>
HDF5_INSTALL_BIN_DIR "bin"
HDF5_INSTALL_LIB_DIR "lib"
HDF5_INSTALL_INCLUDE_DIR "include"
HDF5_INSTALL_MODULE_DIR "mod"
HDF5_INSTALL_CMAKE_DIR "cmake"
if (MSVC)
HDF5_INSTALL_DATA_DIR "."
else ()
HDF5_INSTALL_DATA_DIR "share"
HDF5_INSTALL_DOC_DIR "HDF5_INSTALL_DATA_DIR"
HDF5_USE_GNU_DIRS "ON to use GNU Coding Standard install directory variables,
OFF to use historical settings" OFF
Defaults as defined by the 'GNU Coding Standards'
HDF5_INSTALL_BIN_DIR "bin"
HDF5_INSTALL_LIB_DIR "lib"
HDF5_INSTALL_INCLUDE_DIR "include"
HDF5_INSTALL_MODULE_DIR "HDF5_INSTALL_INCLUDE_DIR/mod"
HDF5_INSTALL_CMAKE_DIR "HDF5_INSTALL_LIB_DIR/cmake"
HDF5_INSTALL_DATA_DIR "share"
HDF5_INSTALL_DOC_DIR "HDF5_INSTALL_DATA_DIR/doc/hdf5"
---------------- HDF5 Advanced Options ---------------------
HDF5_ONLY_SHARED_LIBS "Only Build Shared Libraries" OFF
HDF5_ALLOW_UNSUPPORTED "Allow unsupported combinations of configure options" OFF
HDF5_ENABLE_PARALLEL "Enable parallel build (requires MPI)" OFF
HDF5_ENABLE_THREADSAFE "Enable Threadsafety" OFF
HDF5_ENABLE_CONCURRENCY "Enable multi-threaded concurrency" OFF
HDF5_DIMENSION_SCALES_NEW_REF "Use new-style references with dimension scale APIs" OFF
HDF5_EXTERNAL_LIB_PREFIX "Use prefix for custom library naming." ""
HDF5_EXTERNAL_LIB_SUFFIX "Use suffix for custom library naming." ""
HDF5_DISABLE_COMPILER_WARNINGS "Disable compiler warnings" OFF
HDF5_ENABLE_ALL_WARNINGS "Enable all warnings" OFF
HDF5_SHOW_ALL_WARNINGS "Show all warnings (i.e. not suppress "noisy" ones internally)" OFF
HDF5_ENABLE_COVERAGE "Enable code coverage for Libraries and Programs" OFF
HDF5_ENABLE_DEBUG_APIS "Turn on extra debug output in all packages" OFF
HDF5_ENABLE_DEPRECATED_SYMBOLS "Enable deprecated public API symbols" ON
HDF5_ENABLE_EMBEDDED_LIBINFO "embed library info into executables" ON
HDF5_ENABLE_PREADWRITE "Use pread/pwrite in sec2/log/core VFDs in place of read/write (when available)" ON
HDF5_ENABLE_TRACE "Enable API tracing capability" OFF
HDF5_ENABLE_USING_MEMCHECKER "Indicate that a memory checker is used" OFF
HDF5_ENABLE_MAP_API "Build the map API" OFF
HDF5_GENERATE_HEADERS "Rebuild Generated Files" OFF
HDF5_JAVA_PACK_JRE "Package a JRE installer directory" OFF
HDF5_NO_PACKAGES "Do not include CPack Packaging" OFF
HDF5_PACK_EXAMPLES "Package the HDF5 Library Examples Compressed File" OFF
HDF5_PACK_MACOSX_FRAMEWORK "Package the HDF5 Library in a Frameworks" OFF
HDF5_BUILD_FRAMEWORKS "TRUE to build as frameworks libraries,
FALSE to build according to BUILD_SHARED_LIBS" FALSE
HDF5_PACKAGE_EXTLIBS "CPACK - include external libraries" OFF
HDF5_STRICT_FORMAT_CHECKS "Whether to perform strict file format checks" OFF
HDF5_WANT_DATA_ACCURACY "IF data accuracy is guaranteed during data conversions" ON
HDF5_WANT_DCONV_EXCEPTION "exception handling functions is checked during data conversions" ON
HDF5_DEFAULT_API_VERSION "Enable default API (v16, v18, v110, v112, v114, v200)" "v200"
HDF5_USE_FOLDERS "Enable folder grouping of projects in IDEs." ON
HDF5_MSVC_NAMING_CONVENTION "Use MSVC Naming conventions for Shared Libraries" OFF
HDF5_MINGW_STATIC_GCC_LIBS "Statically link libgcc/libstdc++" OFF
if (APPLE)
HDF5_BUILD_WITH_INSTALL_NAME "Build with library install_name set to the installation path" OFF
if (CMAKE_BUILD_TYPE MATCHES Debug)
HDF5_ENABLE_INSTRUMENT "Instrument The library" OFF
if (HDF5_BUILD_FORTRAN)
HDF5_INSTALL_MOD_FORTRAN "Copy FORTRAN mod files to include directory (NO SHARED STATIC)" SHARED
if (BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is SHARED
if (BUILD_SHARED_LIBS AND NOT BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is SHARED
if (NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is STATIC
if (NOT BUILD_SHARED_LIBS AND NOT BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is SHARED
HDF5_ENABLE_ANALYZER_TOOLS "enable the use of Clang tools" OFF
HDF5_ENABLE_SANITIZERS "execute the Clang sanitizer" OFF
HDF5_ENABLE_FORMATTERS "format source files" OFF
HDF5_BUILD_DOC "Build documentation" OFF
HDF5_ENABLE_DOXY_WARNINGS "Enable fail if doxygen parsing has warnings." OFF
HDF5_H5CC_C_COMPILER "C compiler to use in h5cc" ${CMAKE_C_COMPILER}
HDF5_H5CC_CXX_COMPILER "C++ compiler to use in h5cc" ${CMAKE_CXX_COMPILER}
HDF5_H5CC_Fortran_COMPILER "Fortran compiler to use in h5cc" ${CMAKE_Fortran_COMPILER}
---------------- HDF5 VFD Options ---------------------
HDF5_ENABLE_DIRECT_VFD "Build the Direct I/O Virtual File Driver" OFF
HDF5_ENABLE_MIRROR_VFD "Build the Mirror Virtual File Driver" OFF
HDF5_ENABLE_ROS3_VFD "Build the ROS3 Virtual File Driver" OFF
HDF5_ENABLE_HDFS "Enable HDFS" OFF
HDF5_ENABLE_SUBFILING_VFD "Build Parallel HDF5 Subfiling VFD" OFF
---------------- HDF5 Advanced Test Options ---------------------
if (BUILD_TESTING)
HDF5_TEST_SERIAL "Execute non-parallel tests" ON
HDF5_TEST_TOOLS "Execute tools tests" ON
HDF5_TEST_EXAMPLES "Execute tests on examples" ON
HDF5_TEST_SWMR "Execute SWMR tests" ON
HDF5_TEST_PARALLEL "Execute parallel tests" ON
HDF5_TEST_FORTRAN "Execute fortran tests" ON
HDF5_TEST_CPP "Execute cpp tests" ON
HDF5_TEST_JAVA "Execute java tests" ON
HDF_TEST_EXPRESS "Control testing framework (0-3)" "3"
HDF5_TEST_PASSTHROUGH_VOL "Execute tests with different passthrough VOL connectors" OFF
if (HDF5_TEST_PASSTHROUGH_VOL)
HDF5_TEST_FHEAP_PASSTHROUGH_VOL "Execute fheap test with different passthrough VOL connectors" ON
HDF5_TEST_VFD "Execute tests with different VFDs" OFF
if (HDF5_TEST_VFD)
HDF5_TEST_FHEAP_VFD "Execute fheap test with different VFDs" ON
HDF5_TEST_SHELL_SCRIPTS "Enable shell script tests" ON
HDF5_DISABLE_TESTS_REGEX "Regex pattern to set execution of specific tests to DISABLED" ""
HDF5_USING_ANALYSIS_TOOL "Indicate that an analysis checker is used" ON
---------------- External Library Options ---------------------
HDF5_ALLOW_EXTERNAL_SUPPORT "Allow External Library Building (NO GIT TGZ)" "NO"
HDF5_ENABLE_PLUGIN_SUPPORT "Enable PLUGIN Filters" OFF
HDF5_ENABLE_SZIP_SUPPORT "Use SZip Filter" OFF
HDF5_MODULE_MODE_ZLIB "Prefer module mode to find ZLIB" ON
HDF5_ENABLE_ZLIB_SUPPORT "Enable Zlib Filters" OFF
if (HDF5_USE_ZLIB_NG)
ZLIBNG_USE_EXTERNAL "Use External Library Building for ZLIBNG" OFF
ZLIBNG_TGZ_ORIGPATH "Use ZLIBNG from original location" "https://github.com/zlib-ng/zlib-ng/releases/tag/2.2.4"
ZLIBNG_TGZ_NAME "Use ZLIBNG from original compressed file" "2.2.4.tar.gz"
else
ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" OFF
ZLIB_TGZ_ORIGPATH "Use ZLIB from original location" "https://github.com/madler/zlib/releases/download/v1.3.1"
ZLIB_TGZ_NAME "Use ZLIB from original compressed file" "zlib-1.3.1.tar.gz"
ZLIB_USE_LOCALCONTENT "Use local file for ZLIB FetchContent" OFF
HDF5_USE_ZLIB_STATIC "Find static zlib library" OFF
SZIP_USE_EXTERNAL "Use External Library Building for SZIP else search" OFF
if (HDF5_ENABLE_SZIP_SUPPORT)
HDF5_ENABLE_SZIP_ENCODING "Use SZip Encoding" ON
LIBAEC_TGZ_ORIGPATH "Use LIBAEC from original location" "https://github.com/MathisRosenhauer/libaec/releases/download/v1.1.3"
LIBAEC_TGZ_NAME "Use LIBAEC from original compressed file" "libaec-1.1.3.tar.gz"
LIBAEC_USE_LOCALCONTENT "Use local file for LIBAEC FetchContent" OFF
HDF5_USE_LIBAEC_STATIC "Find static AEC library" OFF
PLUGIN_USE_EXTERNAL "Use External Library Building for PLUGINS else search" OFF
PLUGIN_TGZ_ORIGPATH "Use PLUGIN from original location" "https://github.com/HDFGroup/hdf5_plugins/releases/download/snapshot"
PLUGIN_TGZ_NAME "Use PLUGIN from original compressed file" "hdf5_plugins-master.tar.gz"
PLUGIN_USE_LOCALCONTENT "Use local file for PLUGIN FetchContent" OFF
if (WINDOWS)
H5_DEFAULT_PLUGINDIR "%ALLUSERSPROFILE%/hdf5/lib/plugin"
else ()
H5_DEFAULT_PLUGINDIR "/usr/local/hdf5/lib/plugin"
endif ()
NOTE:
The BUILD_STATIC_EXECS ("Build Static Executables") option is only valid
on some unix operating systems. It adds the "-static" flag to cflags. This
flag is not available on windows and some modern linux systems will
ignore the flag.
NOTE:
The HDF5_USE_GNU_DIRS option is usually recommended for linux platforms, but may
be useful on other platforms. See the CMake documentation for more details.
---------------- Unsupported Library Options ---------------------
The threadsafe, C++ and Java interfaces are not compatible
with the HDF5_ENABLE_PARALLEL option.
Unless HDF5_ALLOW_UNSUPPORTED has been specified,
the following options must be disabled:
HDF5_ENABLE_THREADSAFE, HDF5_BUILD_CPP_LIB, HDF5_BUILD_JAVA
The high-level, C++, Fortran and Java interfaces are not compatible
with the HDF5_ENABLE_THREADSAFE option because the lock is not hoisted
into the higher-level API calls. Unless HDF5_ALLOW_UNSUPPORTED has been
specified, the following options must be disabled:
HDF5_BUILD_HL_LIB, HDF5_BUILD_CPP_LIB, HDF5_BUILD_FORTRAN, HDF5_BUILD_JAVA
The multi-threaded concurrency and threadsafe options are mutually
exclusive, only one or the other may be enabled.
The multi-threaded concurrency, C++, and Java interfaces are not compatible
with the HDF5_ENABLE_PARALLEL option.
Unless HDF5_ALLOW_UNSUPPORTED has been specified,
the following options must be disabled:
HDF5_ENABLE_CONCURRENCY, HDF5_BUILD_CPP_LIB, HDF5_BUILD_JAVA
The high-level, C++, Fortran, and Java interfaces are not compatible
with the HDF5_ENABLE_CONCURRENCY option because the lock is not hoisted
into the higher-level API calls. Unless HDF5_ALLOW_UNSUPPORTED has been
specified, the following options must be disabled:
HDF5_BUILD_HL_LIB, HDF5_BUILD_CPP_LIB, HDF5_BUILD_FORTRAN, HDF5_BUILD_JAVA
========================================================================
VIII. User Defined Options for HDF5 Libraries with CMake
========================================================================
Support for User Defined macros and options has been added. The file
UserMacros.cmake has an example of the technique.
Replace the template code with your macro in the UserMacros.cmake file.
Then enable the option to the CMake configuration, build and test process.
========================================================================
IX. User Defined Compile Flags for HDF5 Libraries with CMake
========================================================================
Custom compiler flags can be added by defining the CMAKE_C_FLAGS and
CMAKE_CXX_FLAGS variables.
Using a cmake script:
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O2")
Defined on the configure line:
cmake -G "Visual Studio 17 2019" -DCMAKE_C_FLAGS:STRING=-O2 ..
Debug symbols are enabled with configuration selections Debug or RelWithDebInfo.
The difference between Debug and RelWithDebInfo configurations is that
RelWithDebInfo optimizes the code similar to Release. It produces fully optimized
code, but also creates the symbol table and the debug metadata to give the
debugger input to map the execution back to the original code.
RelwithDebInfo configuration should not affect the performance when the code
is run without a debugger attached.
The HDF5_ENABLE_COVERAGE option will add "-g -O0 -fprofile-arcs -ftest-coverage"
to CMAKE_C_FLAGS.
========================================================================
X: Considerations for Cross-Compiling
========================================================================
Cross-compiling has several consequences for CMake:
CMake cannot automatically detect the target platform.
CMake cannot find libraries and headers in the default system directories.
Executables built during cross compiling cannot be executed.
Cross-compiling support means that CMake separates information about the
build platform and target platform and gives the user mechanisms to solve
cross-compiling issues without additional requirements such as running
virtual machines, etc.
CMake uses a toolchain of utilities to compile, link libraries and create
archives, and other tasks to drive the build. The toolchain utilities
available are determined by the languages enabled.
CMake stores info about the current toolchain in the following variables:
CMAKE_C_COMPILER,
CMAKE_CXX_COMPILER.
They contain paths to the C and C++ compilers respectively. This is usually
enough on desktop platforms. In the case of embedded systems, a custom
linker and assembler setting may be needed. In more complex projects
you may need to additionally specify binaries to other parts of the toolchain
(size, ranlib, objcopy…). All these tools should be set in the corresponding
variables:
CMAKE_AR,
CMAKE_ASM_COMPILER,
CMAKE_LINKER,
CMAKE_OBJCOPY,
CMAKE_RANLIB
As for the host and target operating systems, CMake stores their names in the
following variables:
CMAKE_HOST_SYSTEM_NAME – name of the platform, on which CMake is running (host platform).
On major operating systems this is set to the Linux, Windows or
Darwin (MacOS) value.
CMAKE_SYSTEM_NAME – name of the platform, for which we are building (target platform).
By default, this value is the same as CMAKE_HOST_SYSTEM_NAME, which
means that we are building for the local platform (no cross-compilation).
Put the toolchain variables into a separate file (e.g. <toolchain_name>.cmake)
and set CMAKE_TOOLCHAIN_FILE variable to the path of that file.
If cmake is invoked with the command line parameter:
--toolchain path/to/file
or
-DCMAKE_TOOLCHAIN_FILE=path/to/file
the file will be loaded early to set values for the compilers. The
CMAKE_CROSSCOMPILING variable is set to true when CMake is cross-compiling.
Structure of the toolchain file
-------------------------------
In fact, the toolchain file doesn’t have any structure. You can put anything you
want there. But the best practice is to define at least these settings:
path to the toolchain binaries (C compiler, C++ compiler, linker, etc.)
name of the target platform (and optionally target processor architecture)
required compilation and linking flags on that particular platform
toolchain sysroot settings
It is recommended that you set the CMAKE_FIND_ROOT_PATH variable to a path where
you have an exact copy of the root filesystem you have on your target device (with
libraries and binaries pre-compiled for the target processor).
References:
https://cmake.org/cmake/help/latest/manual/cmake-toolchains.7.html
https://gitlab.com/embeddedlinux/libs/platform
https://discourse.cmake.org/t/cross-compile-for-aarch64-on-ubuntu/2161/10
https://stackoverflow.com/questions/54539682/how-to-set-up-cmake-to-cross-compile-with-clang-for-arm-embedded-on-windows?rq=1
https://developer.android.com/ndk/guides/cmake
========================================================================
XI. Creating Custom Preset Configurations
========================================================================
The quickest way to customize your build is to create a CMakeUserPresets.json file
in the HDF5 source directory.
Basic Customization Steps
--------------------------
1. Copy CMakePresets.json to CMakeUserPresets.json:
cp CMakePresets.json CMakeUserPresets.json
2. Edit CMakeUserPresets.json:
- Change configuration names from ci-* to my-*
- Modify the "inherits" field in "configurePresets" for alternate options
- Update "configurePreset" fields in "buildPresets", "testPresets", "packagePresets"
- Update names in "workflowPresets" steps from ci-* to my-*
Example: Using Local Support Files
-----------------------------------
To change external support files to use a local directory:
{
"name": "my-base-tgz",
"hidden": true,
"inherits": "ci-base",
"cacheVariables": {
"HDF5_ALLOW_EXTERNAL_SUPPORT": {"type": "STRING", "value": "TGZ"},
"TGZPATH": {"type": "PATH", "value": "${sourceParentDir}/temp"}
}
},
{
"name": "my-StdCompression",
"hidden": true,
"inherits": "my-base-tgz",
"cacheVariables": {
...
}
},
{
"name": "my-StdShar",
"hidden": true,
"inherits": "my-StdCompression",
"cacheVariables": {
...
}
},
{
"name": "my-StdShar-GNUC",
"description": "My Custom GNUC Standard Config for x64 (Release)",
"inherits": [
"ci-x64-Release-GNUC",
"ci-CPP",
"ci-Fortran",
"ci-Java",
"my-StdShar",
"my-StdExamples"
]
}
Then you can change or add options for your specific case.
Maven Deployment Preset Example
--------------------------------
For Maven deployment with custom repository URL:
{
"name": "my-maven-custom",
"inherits": "ci-MinShar-GNUC-Maven-Snapshot",
"cacheVariables": {
"MAVEN_REPOSITORY_URL": {"type": "STRING", "value": "https://your-repo.com/maven"},
"HDF5_ENABLE_ROS3_VFD": {"type": "BOOL", "value": "ON"}
}
}
Then build with:
cmake --workflow --preset my-maven-custom --fresh
Note: This example uses JNI (default). For FFM, inherit from ci-MinShar-GNUC-Maven-FFM-Snapshot
Preset File Details
-------------------
CMakePresets.json and CMakeUserPresets.json:
- Live in the project's root directory
- Both have the same format
- CMakePresets.json: Project-wide build details (don't modify)
- CMakeUserPresets.json: Your local build customizations
The HDF Group presets require CMake 3.26 and use the Ninja build system.
Ninja may need to be installed separately on some platforms.
Hidden presets (marked "hidden": true) are used for inheritance and
cannot be used directly. They are defined in config/cmake-presets/hidden-presets.json.
For more information:
https://cmake.org/cmake/help/latest/manual/cmake-presets.7.html
========================================================================
XII. Using the Library
========================================================================
For information on using HDF5 see the documentation, tutorials and examples
found here:
https://support.hdfgroup.org/documentation/index.html
A summary of the features included in the built HDF5 installation can be found
in the libhdf5.settings file in the same directory as the static and/or
shared HDF5 libraries. However CMake provides a programmable method to
determine the features of the library. The CMake installation will
provide a CMake package configuration file, located in the installation folder,
cmake/hdf5-config.cmake, and can be used to determine the features of the library.
The file is accessed by using the find_package command in your CMakeLists.txt file.
1. 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
(Note there are no quote characters used on Windows and all platforms
use forward slashes)
2. Add the following to your CMakeLists.txt file:
find_package (HDF5 NAMES hdf5 COMPONENTS C shared)
The components are optional and can be omitted if not needed. The
components are: shared, static, C, CXX, Fortran, HL, Java, Tools, and VOL.
========================================================================
XIII. Using CMake Regex Options for Testing
========================================================================
CMake provides a way to use regular expressions to control which tests are
executed. The HDF5 CMake build system provides labels for each test that
can be used to select tests. The labels are defined in the CMakeTests.cmake
files.
Some of the labels are:
PARALLEL
- MPI_TEST for parallel tests.
- MPI_TEST_FORT for just parallel Fortran tests.
SERIAL
- CPP for C++ tests.
- HL_CPP for high-level C++ tests.
- FORTRAN for Fortran tests.
- HL_FORTRAN for high-level Fortran tests.
- HL for high-level tests.
- JUnit for Java tests.
- H5WATCH for tests that use the h5watch SWMR program.
- SWMR for tests that use the SWMR feature.
- h5_api for the API tests.
- VOL for tests that use the VOL feature.
- VFD for tests that use the VFD feature.
- H5TEST for the library tests.
- EX for examples
- H5CLEAR for the h5clear tool tests.
- H5COPY for the h5copy tool tests.
- H5DIFF for the h5diff tool tests.
- H5DUMP for the h5dump tool tests.
- H5FC for the h5fc tool tests.
- H5IMPORT for the h5import tool tests.
- H5JAM for the h5jam tool tests.
- H5LS for the h5ls tool tests.
- H5MKGRP for the h5mkgrp tool tests.
- H5REPACK for the h5repack tool tests.
- H5REPART for the h5repart tool tests.
- H5STAT for the h5stat tool tests.
- PERFORM for performance tests.
To run tests with a specific label, use the --tests-regex (or -R) option with ctest.
For example, to run only the C++ tests, use:
ctest . --tests-regex "CPP"
To run tests with multiple labels, use the | operator to separate the labels.
To run tests with the MPI_TEST and FORTRAN labels, use:
ctest . --tests-regex "MPI_TEST|FORTRAN"
To run tests and exclude tests with a specific label, use the
--exclude-regex (or -E) option with ctest.
For more information on using regular expressions with ctest,
see the CMake documentation:
https://cmake.org/cmake/help/latest/manual/ctest.1.html#regular-expressions
========================================================================
XIV. Java FFM Testing
========================================================================
HDF5 2.0 includes comprehensive Foreign Function & Memory (FFM) API tests
for Java 25+.
FFM Test Organization
---------------------
Tests are organized by HDF5 module in java/jtest/:
Module Test Files:
- TestH5ffm.java - General library operations
H5open, H5close, memory management, version info
- TestH5Affm.java - Attribute operations
- TestH5Dffm.java - Dataset operations
- TestH5Effm.java - Error handling
- TestH5Fffm.java - File operations
- TestH5FDffm.java - File drivers
- TestH5Gffm.java - Group operations
- TestH5Iffm.java - Identifier management
- TestH5Lffm.java - Link operations
- TestH5Offm.java - Object operations
- TestH5Pffm.java - Property lists
- TestH5PLffm.java - Plugin management
- TestH5Rffm.java - References
- TestH5Sffm.java - Dataspace operations
- TestH5Tffm.java - Datatype operations
- TestH5VLffm.java - VOL connector
- TestH5Zffm.java - Filter operations
Running FFM Tests
-----------------
To run all FFM tests:
ctest -R "JUnitFFM" -V
To run specific module tests:
ctest -R "JUnit-TestH5Affm" -V # Attributes
ctest -R "JUnit-TestH5Pffm" -V # Properties
ctest -R "JUnit-TestH5Tffm" -V # Datatypes
ctest -R "JUnit-TestH5Sffm" -V # Dataspaces
Test Requirements:
- Java 25+ with --enable-native-access=ALL-UNNAMED
- FFM bindings JAR (javahdf5-*.jar)
- JUnit 4.x test framework
- HDF5 native libraries in LD_LIBRARY_PATH
FFM Test Patterns:
- All tests use Arena.ofConfined() for memory management
- Proper cleanup in try-with-resources blocks
- Return value checking with isSuccess() / isValidId()
- See java/jtest/FfmTestSupport.java for utility methods
ROS3 VFD (S3 Cloud Storage):
- Tests are compatible with both plain and ROS3-enabled builds
- Use -DHDF5_ENABLE_ROS3_VFD=ON with any Maven preset for ROS3 builds
- Example: cmake --preset ci-MinShar-GNUC-Maven -DHDF5_ENABLE_ROS3_VFD=ON
- Same test suite validates both feature sets
========================================================================
For further assistance, send email to help@hdfgroup.org
========================================================================
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