Scot Breitenfeld
d8ec63966c
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.
HDF5 Examples
Please refer to the Using_CMake.txt file for CMake instructions.
Note that this HDF5Examples directory structure is also provided as a stand-alone project distributed with library binaries as well as compiled and tested during a HDF5 Library build.
This repository contains a high-performance library's example code that demonstrate the HDF5® data model API. The HDF5® data model has been adopted across many industries and this implementation has become a de facto data management standard in science, engineering, and research communities worldwide.
The HDF Group is the developer, maintainer, and steward of HDF5 software. Find more information about The HDF Group, the HDF5 Community, and other HDF5 software projects, tools, and services at The HDF Group's website.
We suggest using the presets method with CMake for building the examples. However, if you prefer to use the h5cc pkg-config wrappers, you can use the following commands to build the examples:
export HDF5_HOME="hdf5 installation root"
export PKG_CONFIG_PATH="$HDF5_HOME/lib/pkgconfig"
export LD_LIBRARY_PATH="$HDF5_HOME/lib:$LD_LIBRARY_PATH"
export PATH="$HDF5_HOME/bin:$PATH"
Then, you can compile the examples with:
h5cc -o example1 example1.c
h5c++ -o example2 example2.cpp
h5fc -o example3 example3.f90
For Java examples with Maven integration, see the JAVA/README-MAVEN.md file for complete instructions on using the org.hdfgroup:hdf5-java-examples Maven artifact.
The test-pc.sh script can test the examples with the h5*cc pkg-config wrappers with: cd <path to examples> export HDF5_HOME="hdf5 installation root"; sh ./test-pc.sh <path to examples> <path to build dir> . Notice that period (.) at the end of the command is important, it tells the script to use the current directory as the source directory.
HELP AND SUPPORT
Information regarding Help Desk and Support services is available at
FORUM and NEWS
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News and Announcements https://forum.hdfgroup.org/c/news-and-announcements-from-the-hdf-group
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HDF5 SNAPSHOTS, PREVIOUS RELEASES AND SOURCE CODE
Full Documentation and Programming Resources for this HDF5 can be found at
https://support.hdfgroup.org/documentation/index.html
Periodically development code snapshots are provided at the following URL:
https://github.com/HDFGroup/hdf5/releases/tag/snapshot
Source packages for current and previous releases are located at:
Latest HDF5 release Previous releases
Development code is available at our Github location: