The Fortran example set sel_type = H5S_BLOCK_F on the branch where a rank
calls H5Sselect_none (no data to contribute) and H5S_ALL_F on the branch
where a rank sets a real hyperslab, which is backwards. The equivalent C
example (ph5_filtered_writes_no_sel.c) does the opposite:
H5Dwrite(..., no_selection ? H5S_ALL : H5S_BLOCK, ...);
i.e. H5S_ALL when there is no selection (mirrors the file dataspace's own
empty selection) and H5S_BLOCK when a hyperslab was set (memory buffer
matches the block shape of the file selection).
With the inversion, H5Dwrite_f feeds a bogus selection into the collective
filtered I/O path, corrupting the element/byte-length accounting in
H5D__mpio_collective_filtered_chunk_update, which segfaults inside
H5D_select_io_mem -> H5VM_memcpyvv on 12 MPI ranks. Reproduces on current
develop; the bug has been present since the example was added in #3916.
* Fix MPI Fortran configuration for HDF5Examples (#6205)
When building Fortran parallel examples standalone without MPI
wrappers, the compiler cannot find mpi.mod because
MPI_Fortran_INCLUDE_DIRS is not populated.
* Use MPI::MPI_Fortran imported target instead of raw MPI variables
Replace manual MPI_Fortran_LIBRARIES, MPI_Fortran_LINK_FLAGS, and
MPI_Fortran_INCLUDE_DIRS usage with the MPI::MPI_Fortran imported
target, which transitively carries all include dirs, compile flags,
and link flags. This eliminates the CMAKE_Fortran_EXE_LINKER_FLAGS
hack and the manual target_include_directories in H5PAR.
Renamed all HDF5 examples build options from H5EX_* to H5EXAMPLE_* to better distinguish them from library options when building examples alongside the library.
Updated all CMake files, including:
Main examples CMakeLists.txt files
CMake configuration files in config/ directory
CMake preset files
Updated documentation files to reflect new option names
This update systematically renames variables across 2.0+ CMake files in the HDF5Examples directory and configuration templates. The goal is to change variables from sounding like build "options" (e.g., HDF5_BUILD_TOOLS, HDF5_ENABLE_PARALLEL) to reflecting library "state" (e.g., what features the installed library provides).
* Cleanup threads package checks
* Check first if package was found
* Remove unnecessary dependent checks
* Remove Unused options and fix names of option prefix
* addressed issue wit promoted integers and reals
* fixed h5fcreate_f
* added option to use mpi_f08
* change the kind of logical in the parallel tests
* addressed missing return value from callback
With MPI 4.1 the use of the mpif.h include file has been deprecated. Codes
should transition to USE mpi or USE mpi_f08.
Signed-off-by: Christoph Niethammer <niethammer@hlrs.de>
* Merge examples repo into library
* Change grepTest to be more fault-tolerant
* Update examples macro file
* Exclude all Fortran examples from doxygen
Scot Breitenfeld
jhendersonHDF
Allen Byrne
Christoph Niethammer