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HDF5 - hierarchical data format

Documentation

HDF5 is a data model, library, and file format for storing and managing data. It can represent very complex data objects and a wide variety of metadata.

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Documentation

For a documentation visit the HDF groupImage Removed support portal

Documentation

Installed versions

Serial HDF-5

Installed versions

We cannot support all combinations of hdf5, compiler and mpi. If none of the installed version works, please contact support for installation of missing versions.

Serial HDF-5

VersionCompilerModuleAPI
1.10.5intel/18.0.6hdf5/intel/1.10.5v110
1.10.5gcc/7.5.0hdf5/gcc.7/1.10.5v110
1.10.5gcc/8.3.0hdf5/gcc.8/1.10.5v110
1.10.6gcc/8.3.0hdf5/gcc.8/1.10.6v110
1.10.7gcc/9.3.0hdf5/gcc.9/1.10.7v110
1.12.1intel/19.0.5hdf5/intel/1.12.1v112
1.12.2gcc/8.3.0hdf5/gcc.8/1.12.2v112
1.12.2gcc/9.3.0hdf5/gcc.9/1.12.2v112
1.12.2intel/2022.2hdf5/intel/1.12.2v112

Parallel HDF-5

VersionCompiler, MPIModuleAPI
1.10.5intel/18.0.6, impi/2018.5hdf5-parallel/impi/intel/1.10.5v110
1.1012.60intel/1819.01.62, impi/20182019.58hdf5-parallel/impi/intel/1.1012.60v110v112

1.10.6

intel/18.0.6, openmpi/intel/3.1.6

hdf5-parallel/ompi/intel/1.10.6v110

1.10.5

gcc/8.3.0, openmpi/gcc.9/3.1.5

hdf5-parallel/ompi/gcc.8/1.10.5v110

1.10.6

gcc/9.2.0, openmpi/gcc.9/3.1.5hdf5-parallel/ompi/gcc.9/1.10.6v110
1.12.01gcc/8.3.0, openmpi/gcc.9/3.1.5hdf5-parallel/ompi/gcc.8/1.12.0v112

The libraries are threadsafe and can be used in omp-parallel codes. To see configure-details on the installed libraries, load a hdf5-module and issue cat $HDF5DIR/libhdf5.settings!

obsolete versions

Modules and Prerequisites

  • module avail hdf5 shows all available hdf5 versions
  • module show <modulename> shows environment variables set when loading the module
  • module help <modulename>shows some details on compilers and MPI

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  • readelf -a $HDF5DIR/libhdf5_hl.so | grep RPATH

Linking the hdf5-libraries in user programs

Loading a hdf5-module does not link the libraries automatically, when compiling some other software. hdf5 does not deliver any standard way to detect the path to the libraries like pkg-config. So you have to configure Makefiles or install-scripts "by hand". The environment variables exported by the modules should allow short and flexible notation.

hdf5-modules do not have any effect during the runtime of your binaries. If the hdf5-libraries are linked dynamically, it is recommended to set RPATH in the binary. Otherwise the hdf5-libraries (and others) will not be found, during runtime. This can be done with the compiler option -Wl,-rpath=$LD_RUN_PATH, which passes the rpath to the linker.

hdf5 compiler wrapper

The compiler wrapper h5cc, h5fc (parallel h5pcc and h5pfc) can be used to build programs linking the hdf5-libraries. These wrappers set rpath for all libraries to be linked dynamically for hdf5.

Installing the hdf5-libraries at HLRN

Read more