BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems

The motivation of this work is that BioFVM (http://BioFVM.MathCancer.org) supports only on-node shared memory parallelism using OpenMP. We have developed BioFVM_X as it adds MPI to BioFVM to parallelize the core kernels of BioFVM using MPI. Some core kernels are Domain Partitioning, Basic Agent Generation, Gaussian Profile building, File Writing, Direct Solver (Thomas' algorithm). Most of the MPI-based parallel functions are made available in BioFVM_parallel.cpp.