HDF

HDF (Hierarchical Data Format) is a multi-object file format that facilitates the transfer of various types of scientific data between machines and operating systems.

HDF5 is installed on : blacklight and warhol.

All HDF routines require the header "hdf.h" to be included.

Blacklight Usage

1. Create a batch script to
   1. Set up the module command
   2. Load the HDF module

      module load hdf5

   3. Compile your code, using h5cc (for C) or h5fc (for Fortran). Both compilers are available on blacklight.

      h5cc code.c 

2. Submit the job with the qsub command

See some example jobs.

Warhol Usage

HDF5 code must be compiled on the login nodes on warhol. Several modules must be loaded before you can successfully compile.

To run HDF5 on warhol

1. Load these modules while on the login nodes

   module unload openmpi_gcc
   module load icc
   module load ifort
   module load mvapich2_intel
   module load hdf5
   

2. Compile your C code with h5pcc, or a Fortran code with h5pfc, while on the login nodes


3. Create a batch job which
   1. Loads the hdf5 and ifort modules
   2. Runs the program


4. Submit the job with the qsub command

See the sample job.