Adding Parallel I/O to PARA-BMU

Nick Johnson, Iain Bethune,

EPCC, The University of Edinburgh


VOX-FE[1] is a voxel-based bone modelling suite. The solver part of the suite - PARA-BMU - currently uses only serial I/O routines which lead to poor scalability. We enhance the code by adding parallel I/O routines based on the netCDF[2] and HDF5[3] libraries. We demonstrate that this gives a reduction in file sizes of up to 190x and a reduction in wall-clock time of 7x at 512 cores. This paves the way for PARA-BMU to be used effectively on HECToR and allows users to perform research with much larger and more complex models than was previously possible.