mirror of
https://github.com/HDFGroup/hdf5.git
synced 2025-03-13 16:47:58 +08:00
* Take user block into account when returning chunk addresses (#4236) Both H5Dchunk_iter() and H5Dget_chunk_info(_by_coord)() did not take the size of the user block into account when reporting addresses. Since the #1 use of these functions is to root around in the file for the raw data, this is kind of a problem. Fixes GitHub issue #3003 * Fix a minor warning in h5test.c (#4242) * Turn on -Werror for Java in GitHub -Werror workflows (#4243) * Update Windows CI to not install ninja (#4230) * Rework Fortran macros to use the proper code. (#4240) * Correct reference copy for 16 API (#4244) * Determine MPI LOGICAL during build, used in tests. (#4246) * Skip userblock test in chunk_info.c for multi-file VFDs (#4249) * Match generators with real cmake -G output on Windows (#4252) * Add Julia GitHub Actions. (#4123) * Re-revert to using autoreconf in autogen.sh (#4253) We previously tried removing the per-tool invocation of the Autotools and instead simply invoked autoreconf (PR #1906). This was reverted when it turned out that the NAG Fortran compiler had trouble with an undecorated -shared linker flag. It turns out that this is due to a bug in libtool 2.4.2 and earlier. Since this version of libtool is over a decade old, we're un-reverting the change. We've added a release note for anyone who has to build from source on elderly platforms. Fixes #1343 * Rewrite H5T__path_find_real for clarity (#4225) * Move conversion path free logic to helper function * Add tgz extensions on names (#4255) * Remove an error check regarding large cache objects (#4254) * Remove an error check regarding large cache objects In PR#4231 an assert() call was converted to a normal HDF5 error check. It turns out that the original assert() was added by a developer as a way of being alerted that large cache objects existed instead of as a guard against incorrect behavior, making it unnecessary in either debug or release builds. The error check has been removed. * Update RELEASE.txt * File format security issues (#4234) * Add job timeout to cygwin workflow (#4260) * Replace user-define with user-defined (#4261) * Improve the CMake clang -fsanitize=memory flags (#4267) -fsanitize=memory is almost useless without using -fsanitize-memory-track-origins=2 and we shoud probably add -fno-optimize-sibling-calls as well. * Add documentation (H5M) (#4259) * Add documentation (H5P) (#4262) * MPI type correction (#4268) * corrected type for MPI_*_f2c APIs * fixed return type of callback * reset compilation flags of logical test program * Clean up test/cmpd_dtransform.c (#4270) * Clean up test/cmpd_dtransform.c * Fix uninitialized memory warning from sanitizers * FAIL_STACK_ERROR --> TEST_ERROR * Emit output * Delete test file when done * Fix typo * H5Fdelete() --> remove() * Fix uninitialized memory issues in packet table (#4271) * replace deprecated CMAKE_COMPILER_IS_GNU** (#4272) * Prevent stack overflows in H5E__push_stack (#4264) * Minor fixes after merge of file format security fixes (#4263) * Update H5_IS_BUFFER_OVERFLOW to account for 'size' of 0 * Invert a few checks to avoid function call * CHECK --> CHECK_PTR in tmisc.c (#4274) * Add release note for CVE-2017-17507 (#4275) * Update Cygwin installation guide (#4265) * Addresses configuration fortran testing flags (#4276) * turn warnings to errors in fortran configure test * Intel fortran test fix * Merge julia workflows into standard ci format (#4273) * Fix range check in H5_addr_overlap (#4278) When the H5_addr_overlap macro was updated to use H5_RANGE_OVERLAP, it failed to take into account that H5_RANGE_OVERLAP expects the range to be inclusive. This lead to an assertion failure in H5MM_memcpy due to a memcpy operation on overlapping memory. This has been fixed by subtracting 1 from the calculated high bound values passed to H5_RANGE_OVERLAP * Fix potential buffer read overflows in H5PB_read (#4279) H5PB_read previously did not account for the fact that the size of the read it's performing could overflow the page buffer pointer, depending on the calculated offset for the read. This has been fixed by adjusting the size of the read if it's determined that it would overflow the page.
198 lines
8.0 KiB
Plaintext
198 lines
8.0 KiB
Plaintext
************************************************************************
|
|
* Build and Test HDF5 Examples with CMake *
|
|
************************************************************************
|
|
|
|
Notes: This short instruction is written for users who want to quickly build
|
|
HDF5 Examples using the HDF5 binary package using the CMake tools.
|
|
|
|
More information about using CMake can be found at the KitWare
|
|
site, www.cmake.org.
|
|
|
|
CMake uses the command line; however, the visual CMake tool is
|
|
available for the configuration step. The steps are similar for
|
|
all of the operating systems supported by CMake.
|
|
|
|
NOTES:
|
|
1. Using CMake for building and using HDF5 is under active
|
|
development. While we have attempted to provide error-free
|
|
files, please understand that development with CMake has not
|
|
been extensively tested outside of HDF. The CMake specific
|
|
files may change before the next release.
|
|
|
|
2. CMake for HDF5 development should be usable on any system
|
|
where CMake is supported. Please send us any comments on how
|
|
CMake support can be improved on any system.
|
|
|
|
|
|
========================================================================
|
|
I. Preconditions
|
|
========================================================================
|
|
|
|
1. We suggest you obtain the latest CMake for windows from the Kitware
|
|
web site. The HDF5 product requires a minimum CMake version
|
|
of 3.18.
|
|
|
|
2. You have installed the HDF5 library built with CMake, by executing
|
|
the HDF Install Utility (the *.msi file in the binary package for
|
|
Windows or the *.sh on Linux). If you are using a Windows platform,
|
|
you can obtain a pre-built Windows binary from The HDF Group's website
|
|
at www.hdfgroup.org.
|
|
|
|
3. Set the environment variable HDF5_DIR to the installed location of
|
|
the config files for HDF5. On Windows:
|
|
HDF5_ROOT=C:/Program Files/HDF_Group/HDF5/1.y.x/1
|
|
|
|
(Note there are no quote characters used on Windows and all platforms
|
|
use forward slashes)
|
|
|
|
4. Create separate source and build directories.
|
|
(CMake commands are executed in the build directory)
|
|
|
|
|
|
|
|
========================================================================
|
|
II. Building HDF5 Examples with CMake
|
|
========================================================================
|
|
|
|
Go through these steps to build HDF5 applications with CMake.
|
|
|
|
1. Run CMake
|
|
2. Configure the cache settings
|
|
3. Build HDF5 Examples
|
|
4. Test HDF5 Examples.
|
|
|
|
These steps are described in more detail below.
|
|
|
|
|
|
|
|
1. Run CMake
|
|
|
|
The visual CMake executable is named "cmake-gui.exe" on Windows and should be
|
|
available in your Start menu. For Linux, UNIX, and Mac users the
|
|
executable is named "cmake-gui" and can be found where CMake was
|
|
installed.
|
|
|
|
Specify the source and build directories. Make the build and source
|
|
directories different. For example on Windows, if the source is at
|
|
c:\MyHDFstuff\hdf5ex, then use c:\MyHDFstuff\hdf5ex\build or
|
|
c:\MyHDFstuff\build\hdf5ex for the build directory.
|
|
|
|
PREFERRED:
|
|
Users can perform the configuration step without using the visual
|
|
cmake-gui program. The following is an example command line
|
|
configuration step executed within the build directory:
|
|
|
|
cmake -G "<generator>" [-D<options>] <sourcepath>
|
|
|
|
Where <generator> is
|
|
* Borland Makefiles
|
|
* MSYS Makefiles
|
|
* MinGW Makefiles
|
|
* NMake Makefiles
|
|
* Unix Makefiles
|
|
* Visual Studio 15 2017
|
|
* Visual Studio 15 2017 Win64
|
|
* Visual Studio 16 2019
|
|
* Visual Studio 17 2022
|
|
|
|
|
|
<options> is:
|
|
* H5EX_BUILD_TESTING:BOOL=ON
|
|
* BUILD_SHARED_LIBS:BOOL=[ON | OFF]
|
|
* HDF_BUILD_FORTRAN:BOOL=[ON | OFF]
|
|
* HDF_BUILD_JAVA:BOOL=[ON | OFF]
|
|
|
|
if the hdf5 library was built with a namespace (i.e. "hdf5::") add:
|
|
-D HDF5_NAMESPACE:STRING=hdf5::
|
|
|
|
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 15).
|
|
CMake will read in the CMakeLists.txt files from the source directory and
|
|
display options for the HDF5 Examples project. After the first configure you
|
|
can adjust the cache settings and/or specify locations of other programs.
|
|
|
|
Any conflicts or new values will be highlighted by the configure
|
|
process in red. Once you are happy with all the settings and there are no
|
|
more values in red, click the Generate button to produce the appropriate
|
|
build files.
|
|
|
|
On Windows, if you are using a Visual Studio generator, the solution and
|
|
project files will be created in the build folder.
|
|
|
|
On linux, if you are using the Unix Makefiles generator, the Makefiles will
|
|
be created in the build folder.
|
|
|
|
2.2 Alternative command line example on Windows in c:\MyHDFstuff\hdf5ex\build directory:
|
|
|
|
cmake -G "Visual Studio 19" -DH5EX_BUILD_TESTING:BOOL=ON -DBUILD_SHARED_LIBS:BOOL=ON ..
|
|
|
|
3. Build HDF5 examples
|
|
|
|
On Windows, you can build HDF5 examples using either the Visual Studio Environment
|
|
or the command line. The command line is normally used on linux, Unix, and Mac.
|
|
|
|
To build from the command line, navigate to your build directory and
|
|
execute the following:
|
|
|
|
cmake --build . --config {Debug | Release}
|
|
|
|
NOTE: "--config {Debug | Release}" may be optional on your platform. We
|
|
recommend choosing either Debug or Release on Windows. If you are
|
|
using the pre-built binaries from HDF, use Release.
|
|
|
|
3.1 If you wish to use the Visual Studio environment, open the solution
|
|
file in your build directory. Be sure to select either Debug or
|
|
Release and build the solution.
|
|
|
|
4. Test HDF5 Examples.
|
|
|
|
To test the build, navigate to your build directory and execute:
|
|
|
|
ctest . -C {Debug | Release}
|
|
|
|
NOTE: "-C {Debug | Release}" may be optional on your platform. We
|
|
recommend choosing either Debug or Release to match the build
|
|
step on Windows.
|
|
|
|
5. The files that support building with CMake are all of the files in the
|
|
config/cmake folder, the CMakeLists.txt files in each source folder, and
|
|
CTestConfig.cmake. CTestConfig.cmake is specific to the internal testing
|
|
performed by The HDF Group. It should be altered for the user's
|
|
installation and needs. The cacheinit.cmake file settings are used by
|
|
The HDF Group for daily testing. It should be altered/ignored for the user's
|
|
installation and needs.
|
|
|
|
|
|
|
|
========================================================================
|
|
III. Using HDF5 Libraries with Visual Studio 2008 (no longer supported)
|
|
========================================================================
|
|
|
|
1. Set up path for external libraries and headers
|
|
|
|
Invoke Microsoft Visual Studio and go to "Tools" and select "Options",
|
|
find "Projects", and then "VC++ Directories".
|
|
|
|
1.1 If you are building on 64-bit Windows, find the "Platform" dropdown
|
|
and select "x64".
|
|
|
|
1.2 Find the box "Show directories for", choose "Include files", add the
|
|
header path (i.e. c:\Program Files\HDF Group\HDF5\hdf5-1.8.x\include)
|
|
to the included directories.
|
|
|
|
1.3 Find the box "Show directories for", choose "Library files", add the
|
|
library path (i.e. c:\Program Files\HDF Group\HDF5\hdf5-1.8.x\lib)
|
|
to the library directories.
|
|
|
|
1.4 If using Fortran libraries, you will also need to setup the path
|
|
for the Intel Fortran compiler.
|
|
|
|
|
|
************************************************************************
|
|
|
|
Need further assistance, send email to help@hdfgroup.org
|
|
|