HDF5

Contents

HDF5#

When loaded in conjunction with an MPI module such as openmpi, the hdf5 module provides both the serial and parallel versions of the library.

module load hdf5

module load hdf5/1.10.7

Known issues#

The parallel functionality relies on a technology called MPI-IO, which is currently subject to the following known issue on Bede:

  • HDF5 does not pass all of its parallel tests with OpenMPI 4.x. If you are using this MPI and your application continues to run but does not return from a call to the HDF5 library, you may have hit a similar issue. The current workaround is to instruct OpenMPI to use an alternative MPI-IO implementation with the command: export OMPI_MCA_io=ompio The trade off is that, in some areas, this alternative is extremely slow and so should be used with caution.