HDF

Overview

HDF (Hierarchical Data Format) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of large complex datasets.

The following versions are available:

• v1.8.6 built with the Intel 11.1.064 fortran compiler
• v1.8.7 built with the GNU C compiler
• v1.8.11 built with the Open64 4.5.2 compiler for AMD Bulldozer only
• v1.8.11 built with the PGI 12.10 compiler for AMD Bulldozer only
• v1.8.16 built with the GNU C compiler
• v1.8.16-mpi built with the GNU C compiler, MPI I/O enabled, no C++ interface
• v1.8.16 built with the Intel 15.0.3 C and Fortran compilers

If you require a version compiled with a particular compiler please contact us via its-ri-team@manchester.ac.uk

Restrictions on use

There are no restrictions on access.

Set up procedure

Load one of the following modulefiles to set up your environment:

# Includes MPI I/O support but does not have the C++ interface compiled (a limitation of HDF)
module load apps/gcc/hdf5/1.8.16-mpi
                 #
                 # Before loading this modulefile you should load one of the
                 # following MPI modulefiles:
                 # module load mpi/gcc/openmpi/1.6
                 # module load mpi/gcc/openmpi/1.6-ib


# No MPI I/O support but does have the C++ interface compiled.
module load apps/gcc/hdf5/1.8.16
module load apps/gcc/hdf5/1.8.7

# Older Intel compiler build
module load libs/intel-11.1/hdf/5/1.8.6            # Note the different hdf/5/ naming convention

# Newer Intel compiler build
module load libs/intel-15.0/hdf/t/1.8.16

# Suitable for using on AMD Bulldozer
module load libs/open64-4.5.2/hdf/5/1.8.11         # Note the different hdf/5/ naming convention
module load libs/pgi-12.10/hdf/5/1.8.11-ib-amd-bd  # Note the different hdf/5/ naming convention

Running the application

The modulefiles will set an environement variable named HDF5DIR which can then be used in your compilation process (e.g., in a Makefile) to access the header and library files:

• To inform the compiler of the header file directory use: -I$HDF5DIR/include on the command line
• To inform the compiler of the library files use: -L$HDF5DIR/lib -lhdf5 on the command line
• In a Makefile use $(HDF5DIR) rather than $HDF5DIR.

An example compilation command could be

gcc -I$HDF5DIR/include ex_hdf5.c -o ex_hdf5 -L$HDF5DIR/lib -lhdf5
 #
 # Use mpicc if compiling MPI code that uses the hdf5 library

The HDF ‘bin’ directory is added to your path so that you can access the h5 tools. Use ls $HDF5BIN to see all binary tools.

Further info

Example projects are available in $HDF5DIR/share/hdf5_examples/

See the HDF website for full documentation.

Updates

None.