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hdf5/release_docs/INSTALL_CMake.txt
Dana Robinson 018f093c09
Removes the memory allocation sanity checks feature (#2218) 
* Removes the memory allocation sanity checks feature

* Committing clang-format changes

* Removes zero size checks for H5MM_(c|m)alloc()

* Explicitly return NULL when size == 0 in H5allocate_memory()

* Committing clang-format changes

* Format fix

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-11-03 16:30:08 -07:00

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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: Quick Step Building HDF5 Libraries with CMake Script Mode
Section III: Quick Step Building HDF5 Libraries with CMake Command Mode
Section IV: Further considerations
Section V: Options for building HDF5 Libraries with CMake command line
Section VI: CMake option defaults for HDF5
Section VII: User Defined Options for HDF5 Libraries with CMake
Section VIII: User Defined Compile Flags for HDF5 Libraries with CMake
************************************************************************
========================================================================
I. Preconditions
========================================================================
Obtaining HDF5 source code
1. Create a directory for your development; for example, "myhdfstuff".
2. Obtain compressed (*.tar or *.zip) HDF5 source from
https://portal.hdfgroup.org/display/support/Building+HDF5+with+CMake
and put it in "myhdfstuff".
Uncompress the file. There should be a hdf5-1.13."X" folder.
CMake version
1. We suggest you obtain the latest CMake from the Kitware web site.
The HDF5 1.13."X" product requires a minimum CMake version 3.12,
where "X" is the current HDF5 release version. If you are using
VS2022, the minimum version is 3.21.
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.
========================================================================
II. Quick Step Building HDF5 Libraries with CMake Script Mode
========================================================================
This short set of instructions is written for users who want to quickly
build the HDF5 C and C++ static libraries and tools with SZIP and ZLIB
compression included. This procedure will use the default settings in
the config/cmake/cacheinit.cmake file.
HDF Group recommends using the ctest script mode to build HDF5.
The following files referenced below are available at the HDF web site:
https://portal.hdfgroup.org/display/support/Building+HDF5+with+CMake
Single compressed file with all the files needed, including source:
CMake-hdf5-1.13.X.zip or CMake-hdf5-1.13.X.tar.gz
Individual files included in the above mentioned compressed files
-----------------------------------------------
CMake build script:
CTestScript.cmake
External compression szip and zlib libraries:
LIBAEC.tar.gz
SZip.tar.gz
ZLib.tar.gz
External compression plugin libraries:
hdf5_plugins.tar.gz
Examples Source package:
HDF5Examples-2.0.x-Source.tar.gz
Configuration files:
HDF5config.cmake
HDF5options.cmake
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 the CMake-hdf5-1.13.X.zip(.tar.gz) file to "myhdfstuff".
Uncompress the file.
3. Change to the source directory "hdf5-1.13.x".
CTestScript.cmake file should not be modified.
4. Edit the platform configuration file, HDF5options.cmake, if you want to change
the default build environment.
(See https://portal.hdfgroup.org/display/support/How+to+Change+HDF5+CMake+Build+Options)
5. From the "myhdfstuff" directory execute the CTest Script with the
following options:
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 32-bit Windows with Visual Studio 2015, execute:
ctest -S HDF5config.cmake,BUILD_GENERATOR=VS2015 -C Release -VV -O hdf5.log
On 64-bit Windows with Visual Studio 2015, execute:
ctest -S HDF5config.cmake,BUILD_GENERATOR=VS201564 -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:
HDF5-1.13.NN-<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:
HDF5-1.13."X"-win32.msi or HDF5-1.13."X"-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
----1.13."X"
------bin
------include
------lib
------cmake
On Linux, change to the install destination directory
(create it if doesn't exist) and execute:
<path-to>/myhdfstuff/HDF5-1.13."X"-Linux.sh
After accepting the license, the script will prompt:
By default the HDF5 will be installed in:
"<current directory>/HDF5-1.13."X"-Linux"
Do you want to include the subdirectory HDF5-1.13."X"-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
----1.13."X"
------bin
------include
------lib
------share
On Mac you will find HDF5-1.13."X"-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
----1.13."X"
------bin
------include
------lib
------share
By default the installation will create the bin, include, lib and cmake
folders in the <install destination directory>/HDF_Group/HDF5/1.13."X"
The <install destination directory> depends on the build platform;
Windows will set the default to:
C:/Program Files/HDF_Group/HDF5/1.13."X"
Linux will set the default to:
"myhdfstuff/HDF_Group/HDF5/1.13."X"
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
========================================================================
III. Quick Step Building HDF5 C Static Libraries and Tools with CMake
========================================================================
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 12 2013" -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DHDF5_BUILD_TOOLS:BOOL=ON ..\hdf5-1.13."X"
On Windows 64 bit
cmake -G "Visual Studio 12 2013 Win64" -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DHDF5_BUILD_TOOLS:BOOL=ON ..\hdf5-1.13."X"
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 ../hdf5-1.13."X"
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:
HDF5-1.13."X"-win32.msi or HDF5-1.13."X"-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
----1.13."X"
------bin
------include
------lib
------cmake
On Linux, change to the install destination directory
(create if doesn't exist) and execute:
<path-to>/myhdfstuff/build/HDF5-1.13."X"-Linux.sh
After accepting the license, the script will prompt:
By default the HDF5 will be installed in:
"<current directory>/HDF5-1.13."X"-Linux"
Do you want to include the subdirectory HDF5-1.13."X"-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
----1.13."X"
------bin
------include
------lib
------share
On Mac you will find HDF5-1.13."X"-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
----1.13."X"
------bin
------include
------lib
------share
========================================================================
IV. Further considerations
========================================================================
1. We suggest you obtain the latest CMake for windows from the Kitware
web site. The HDF5 1.13."X" product requires a minimum CMake version 3.18.
2. If you plan to use Zlib or Szip:
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/szlib.lib
-DSZIP_INCLUDE_DIR:PATH=some_location/include
-DSZIP_USE_EXTERNAL:BOOL=OFF
where "some_location" is the full path to the extlibs folder.
Also the appropriate environment variable must be set;
set(ENV{ZLIB_ROOT} "some_location")
set(ENV{SZIP_ROOT} "some_location")
B. Use source packages from an GIT server by adding the following CMake
options:
HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="GIT"
ZLIB_GIT_URL:STRING="http://some_location/zlib"
SZIP_GIT_URL:STRING="http://some_location/szip"
where "some_location" is the URL to the GIT repository. 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"
SZIP_TGZ_NAME:STRING="szip_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.
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"
where "some_location" is the URL to the GIT repository. 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
CMAKE_BUILD_WITH_INSTALL_RPATH:BOOL=OFF
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 12 2013" \
-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF -DHDF5_ENABLE_Z_LIB_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. 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 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.
3. Build and test results can be submitted to our CDash server:
The CDash server for community submissions of hdf5 is at
https://cdash.hdfgroup.org.
Submitters are requested to register their name and contact info and
maintain their test sites. After your first submission, login and go
to your "My CDash" link and claim your site.
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.
4. 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.
========================================================================
V. Options for Building HDF5 Libraries with the 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.
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
* MinGW Makefiles
* NMake Makefiles
* Unix Makefiles
* Visual Studio 14 2015
* Visual Studio 14 2015 Win64
* Visual Studio 15 2017
* Visual Studio 15 2017 Win64
* Visual Studio 16 2019
<options> is:
* SZIP_INCLUDE_DIR:PATH=<path to szip includes directory>
* SZIP_LIBRARY:FILEPATH=<path to szip/library file>
* ZLIB_INCLUDE_DIR:PATH=<path to zlib includes directory>
* ZLIB_LIBRARY:FILEPATH=<path to zlib/library file>
* <HDF5OPTION>:BOOL=[ON | OFF]
<cacheinit.cmake> is:
# This is the CMakeCache file used by HDF Group for daily tests.
########################
# EXTERNAL cache entries
########################
set (CMAKE_INSTALL_FRAMEWORK_PREFIX "Library/Frameworks" CACHE STRING "Frameworks installation directory" FORCE)
set (HDF_PACKAGE_EXT "" CACHE STRING "Name of HDF package extension" FORCE)
set (HDF5_BUILD_FORTRAN ON CACHE BOOL "Build FORTRAN support" FORCE)
set (HDF5_ENABLE_Z_LIB_SUPPORT ON CACHE BOOL "Enable Zlib Filters" FORCE)
set (HDF5_ENABLE_SZIP_SUPPORT ON CACHE BOOL "Use SZip Filter" FORCE)
set (HDF5_ENABLE_SZIP_ENCODING ON CACHE BOOL "Use SZip Encoding" FORCE)
set (MPIEXEC_MAX_NUMPROCS "3" CACHE STRING "Minimum number of processes for HDF parallel tests" FORCE)
set (HDF5_ENABLE_ALL_WARNINGS ON CACHE BOOL "Enable all warnings" FORCE)
set (HDF_TEST_EXPRESS "2" CACHE STRING "Control testing framework (0-3)" FORCE)
set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)" FORCE)
set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ)
set (ZLIB_TGZ_NAME "ZLib.tar.gz" CACHE STRING "Use ZLib from compressed file" FORCE)
set (SZIP_TGZ_NAME "SZip.tar.gz" CACHE STRING "Use SZip from compressed file" FORCE)
set (SZAEC_TGZ_NAME "LIBAEC.tar.gz" CACHE STRING "Use SZip AEC from compressed file" FORCE)
set (USE_LIBAEC ON CACHE BOOL "Use libaec szip replacement" FORCE)
set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of ZLIB package" FORCE)
set (LIBAEC_PACKAGE_NAME "libaec" CACHE STRING "Name of AEC SZIP package" FORCE)
set (SZIP_PACKAGE_NAME "szip" CACHE STRING "Name of SZIP package" FORCE)
#######################
# filter plugin options
#######################
set (PLUGIN_TGZ_NAME "hdf5_plugins.tar.gz" CACHE STRING "Use PLUGINS from compressed file" FORCE)
set (PLUGIN_PACKAGE_NAME "pl" CACHE STRING "Name of PLUGIN package" FORCE)
############
# bitshuffle
###########
set (BSHUF_GIT_URL "https://someurl/bitshuffle.git" CACHE STRING "Use BSHUF from HDF repository" FORCE)
set (BSHUF_GIT_BRANCH "master" CACHE STRING "" FORCE)
set (BSHUF_TGZ_NAME "bitshuffle.tar.gz" CACHE STRING "Use BSHUF from compressed file" FORCE)
set (BSHUF_PACKAGE_NAME "bshuf" CACHE STRING "Name of BSHUF package" FORCE)
#######
# blosc
#######
set (BLOSC_GIT_URL "https://github.com/Blosc/c-blosc.git" CACHE STRING "Use BLOSC from Github" FORCE)
set (BLOSC_GIT_BRANCH "master" CACHE STRING "" FORCE)
set (BLOSC_TGZ_NAME "c-blosc.tar.gz" CACHE STRING "Use BLOSC from compressed file" FORCE)
set (BLOSC_PACKAGE_NAME "blosc" CACHE STRING "Name of BLOSC package" FORCE)
set (ZLIB_GIT_URL "https://someurl/zlib.git" CACHE STRING "Use ZLIB from HDF repo" FORCE)
set (ZLIB_GIT_BRANCH "master" CACHE STRING "" FORCE)
set (ZLIB_TGZ_NAME "ZLib.tar.gz" CACHE STRING "Use ZLib from compressed file" FORCE)
set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of ZLIB package" FORCE)
#######
# bzip2
######
#
set (BZ2_GIT_URL "https://someurl/bzip2.git" CACHE STRING "Use BZ2 from HDF repository" FORCE)
set (BZ2_GIT_BRANCH "master" CACHE STRING "" FORCE)
set (BZ2_TGZ_NAME "BZ2.tar.gz" CACHE STRING "Use BZ2 from compressed file" FORCE)
set (BZ2_PACKAGE_NAME "bz2" CACHE STRING "Name of BZ2 package" FORCE)
#######
# fpzip
#######
set (FPZIP_GIT_URL "https://https://github.com/LLNL/fpzip" CACHE STRING "Use FPZIP from github repository" FORCE)
set (FPZIP_GIT_BRANCH "master" CACHE STRING "" FORCE)
set (FPZIP_TGZ_NAME "fpzip.tar.gz" CACHE STRING "Use FPZIP from compressed file" FORCE)
set (FPZIP_PACKAGE_NAME "fpzip" CACHE STRING "Name of FPZIP package" FORCE)
######
# jpeg
######
set (JPEG_GIT_URL "https://someurl/jpeg.git" CACHE STRING "Use JPEG from HDF repository" FORCE)
set (JPEG_GIT_BRANCH "jpeg9c" CACHE STRING "" FORCE)
#set (JPEG_TGZ_NAME "JPEG9c.tar.gz" CACHE STRING "Use JPEG from compressed file" FORCE)
set (JPEG_TGZ_NAME "JPEG.tar.gz" CACHE STRING "Use JPEG from compressed file" FORCE)
set (JPEG_PACKAGE_NAME "jpeg" CACHE STRING "Name of JPEG package" FORCE)
######
# lz4
######
set (BUILD_LZ4_LIBRARY_SOURCE ON CACHE BOOL "build the lz4 library within the plugin" FORCE)
set (LZ4_GIT_URL "https://someurl/lz4.git" CACHE STRING "Use LZ4 from HDF repository" FORCE)
set (LZ4_GIT_BRANCH "master" CACHE STRING "" FORCE)
set (LZ4_TGZ_NAME "lz4.tar.gz" CACHE STRING "Use LZ4 from compressed file" FORCE)
set (LZ4_PACKAGE_NAME "lz4" CACHE STRING "Name of LZ4 package" FORCE)
######
# lzf
######
set (LZF_GIT_URL "https://someurl/lzf.git" CACHE STRING "Use LZF from HDF repository" FORCE)
set (LZF_GIT_BRANCH "master" CACHE STRING "" FORCE)
set (LZF_TGZ_NAME "lzf.tar.gz" CACHE STRING "Use LZF from compressed file" FORCE)
set (LZF_PACKAGE_NAME "lzf" CACHE STRING "Name of LZF package" FORCE)
########
# mafisc
########
#set (BUILD_MAFISC_LIBRARY_SOURCE OFF CACHE BOOL "build the mafisc library within the plugin" FORCE)
#set (MAFISC_PACKAGE_NAME "mafisc" CACHE STRING "Name of MAFISC package" FORCE)
######
# szf
######
set (SZF_GIT_URL "https://github.com/disheng222/SZ" CACHE STRING "Use SZ from github repository" FORCE)
set (SZF_GIT_BRANCH "master" CACHE STRING "" FORCE)
set (SZF_TGZ_NAME "szf.tar.gz" CACHE STRING "Use SZ from compressed file" FORCE)
set (SZF_PACKAGE_NAME "szf" CACHE STRING "Name of SZ package" FORCE)
######
# zfp
######
set (ZFP_GIT_URL "https://github.com/LLNL/zfp.git" CACHE STRING "Use ZFP from Github" FORCE)
set (ZFP_GIT_BRANCH "master" CACHE STRING "" FORCE)
set (ZFP_TGZ_NAME "zfp.tar.gz" CACHE STRING "Use ZFP from compressed file" FORCE)
set (ZFP_PACKAGE_NAME "zfp" CACHE STRING "Name of ZFP package" 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 12).
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 12 2013" \
-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF -DHDF5_ENABLE_Z_LIB_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 URL (config/cmake/cacheinit.cmake file) are:
ZLIB_GIT_URL:STRING="http://${git_url}/zlib"
SZIP_GIT_URL:STRING="http://${git_url}/szip"
PLUGIN_GIT_URL:STRING="http://${git_url}/plugin"
${git_url} should be changed to your location. 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"
SZIP_TGZ_NAME:STRING="szip_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 USE_LIBAEC option will use the file named by LIBAEC_TGZ_NAME
to build SZIP instead of the file named by SZIP_TGZ_NAME. This option
is also used to account for the different headers and library names.
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.
========================================================================
VI. 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 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
---------------- 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_HL_TOOLS "Build HIGH Level HDF5 Tools" ON
---------------- 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"
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_USE_GNU_DIRS "TRUE to use GNU Coding Standard install directory variables,
FALSE to use historical settings" FALSE
ONLY_SHARED_LIBS "Only Build Shared Libraries" OFF
ALLOW_UNSUPPORTED "Allow unsupported combinations of configure options" OFF
HDF5_EXTERNAL_LIB_PREFIX "Use prefix for custom library naming." ""
HDF5_DISABLE_COMPILER_WARNINGS "Disable compiler warnings" OFF
HDF5_ENABLE_ALL_WARNINGS "Enable all warnings" OFF
HDF5_ENABLE_CODESTACK "Enable the function stack tracing (for developer debugging)." 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_DIRECT_VFD "Build the Direct I/O Virtual File Driver" OFF
HDF5_ENABLE_EMBEDDED_LIBINFO "embed library info into executables" ON
HDF5_ENABLE_PARALLEL "Enable parallel build (requires MPI)" OFF
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_GENERATE_HEADERS "Rebuild Generated Files" ON
HDF5_BUILD_GENERATORS "Build Test Generators" 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
HDF_TEST_EXPRESS "Control testing framework (0-3)" "3"
HDF5_TEST_VFD "Execute tests with different VFDs" OFF
HDF5_TEST_PASSTHROUGH_VOL "Execute tests with different passthrough VOL connectors" OFF
DEFAULT_API_VERSION "Enable default API (v16, v18, v110, v112, v114)" "v114"
HDF5_USE_FOLDERS "Enable folder grouping of projects in IDEs." ON
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_ENABLE_THREADSAFE "Enable Threadsafety" OFF
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_TEST_VFD)
HDF5_TEST_FHEAP_VFD "Execute fheap test with different VFDs" ON
if (HDF5_BUILD_FORTRAN)
HDF5_INSTALL_MOD_FORTRAN "Copy FORTRAN mod files to include directory (NO SHARED STATIC)" "XX"
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_BUILD_DOC "Build documentation" OFF
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
TEST_SHELL_SCRIPTS "Enable shell script tests" 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_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" OFF
PLUGIN_USE_EXTERNAL "Use External Library Building for PLUGINS" 0
ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" 0
SZIP_USE_EXTERNAL "Use External Library Building for SZIP" 0
if (HDF5_ENABLE_SZIP_SUPPORT)
HDF5_ENABLE_SZIP_ENCODING "Use SZip Encoding" OFF
USE_LIBAEC "Use libaec szip replacement" 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 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 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
========================================================================
VII. 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. In the folder,
config/cmake/UserMacros, is an implementation for Windows Visual Studio
users for linking libraries to the static CRT - Windows_MT.cmake.
Copy the contents of the file, both macro and option, into the
UserMacros.cmake file. Then enable the option to the CMake configuration,
build and test process.
========================================================================
VIII. 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 12 2013" -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.
========================================================================
For further assistance, send email to help@hdfgroup.org
========================================================================
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