HDF5 - Hierarchical Data Format

HDF5 is a data model, library, and file format for storing and managing data.



External Links:
HDF5 support page
HDF5: Documentation

Example C code to test HDF5

Here is an example C code that uses the HDF5 library from the HDF5 support website.

To avoid copy/paste errors when using, please copy this from the apps directory:

/usr/local/apps/examples/code/hdf5

Linking HDF5 with Intel compiler

To put the HDF5 libraries in the path for Intel, use

module load hdf5/2.1.1-intel2025-slurm  

To test linking HDF5 with the Intel compiler, compile the example code above, run it, and check that it creates a properly formatted HDF5 file.

[unityID@login]$ cd /share/$GROUP/$USER
[unityID@login]$ cp -r /usr/local/apps/examples/code/hdf5 .
[unityID@login]$ cd hdf5
[unityID@login]$ module purge
[unityID@login]$ module load hdf5/2.1.1-intel2025-slurm
[unityID@login]$ salloc -p compute_partners --ntasks=1 --time=00:10:00 --qos=short
[unityID@compute]$ h5pcc -o test_hdf5_intel h5_crtdat.c
[unityID@compute]$ ./test_hdf5_intel 
[unityID@compute]$ file dset.h5 
dset.h5: Hierarchical Data Format (version 5) data

Notes

HDF5 modules include the MPI libraries (IntelMPI for Intel). After loading the HDF5 module, type module list for the list of other included modules. To use HDF5 with another code, the MPI libraries must be the same.

HDF5 Version 2.1.1

HDF5 2.1.1 was compiled loosely following Section 5 of the README, and using the following CMake configuration settings:

For module:  hdf5/2.1.1-intel2025-slurm

cmake -C ../hdf5-2.1.1/config/cmake/cacheinit.cmake \
      -DCMAKE_BUILD_TYPE:STRING=Release \
      -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/apps/hdf5/2.1.1-intel2025-slurm \
      -DHDF5_ENABLE_PARALLEL:BOOL=ON \
      -DHDF5_BUILD_FORTRAN:BOOL=ON \
      -DHDF5_BUILD_CPP_LIB:BOOL=OFF \
      -DCMAKE_C_COMPILER=mpiicx \
      -DCMAKE_Fortran_COMPILER=mpiifx \
      -DCMAKE_CXX_COMPILER=mpiicpx \
      -DHDF5_BUILD_JAVA:BOOL=OFF \
      -DHDF5_ENABLE_THREADSAFE:BOOL=OFF \
      -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=ON \
      -DZLIB_USE_EXTERNAL:BOOL=OFF \
      -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=ON \
      -DBUILD_SHARED_LIBS:BOOL=ON \
      -DBUILD_STATIC_LIBS:BOOL=OFF \
      -DBUILD_TESTING:BOOL=ON \
      -DHDF5_ENABLE_SUBFILING_VFD:BOOL=ON \
      -DMPIEXEC_EXECUTABLE:STRING=srun \
      -DMPIEXEC_NUMPROC_FLAG:STRING=--ntasks \
      -DMPIEXEC_MAX_NUMPROCS:STRING=6 \
      -G"Unix Makefiles" \
      ../hdf5-2.1.1 >& cmake_configure.mylog &

HDF5 Version 1.14.6

HDF5 1.14.6 was compiled with the following configure flags:

For module:  hdf5/1.14.6-intel2025-slurm

./configure --prefix=/usr/local/apps/hdf5/1.14.6-intel2025-slurm --enable-fortran --enable-hl --enable-parallel CC=mpiicx FC=mpiifx CXX=mpiicpx > configure.mylog 2>&1 &

If an application requires the HDF5 libraries/modules to be compiled with different flags, the user must install a custom version under a space for user maintained software.

Last modified: October 11 2026 11:59:04.