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
module load hdf5
module load hdf5/1.10.11
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=ompioThe trade off is that, in some areas, this alternative is extremely slow and so should be used with caution.