VOX-FE is a voxel-based finite element bone modelling suite developed by Prof. Michael Fagan's Medical & Biological Engineering group at the University of Hull. It is one of the demonstrator applications for the EPSRC-funded "Novel Asynchronous Algorithms and Software for Large Sparse Systems" project, and the core algorithms of VOX-FE are being redeveloped for increased scalability and functionality. The VOX-FE suite comprises two parts; a GUI for manipulating bone structures and visualizing the results of applying strain forces, and an MPI-parallelised Finite Element solver PARA-BMU which performs the computation required to solve the Linear Elasticity problem and calculate stresses and strains in the bone. Example applications would include computing the maximum principal strain in a human mandible (jaw bone) undergoing incisor biting, or understanding the stresses in an axially loaded femur.
Initail examination of the code revealed that plain ASCII files were being used for both input and output data. These were read and written in serial by a single process whereas the solver routines operated in parallel. This solution did not scale well to a large number of cores with the result that for systems with a very large number of finite elements, the runtime was dominated by I/O and MPI data exchange rather than by computation. Another side-effect of using plain text files is that file sizes grow extremely large as the problem size increases which increases transfer times to and from HECToR. Prof. Fagan's group intend to routinely study bone models with resolutions of over 100 million elements in the near future, where the input files are expected to be many GB in size.