BioFVM-X: an MPI+OpenMP 3-D simulator for biological systems

Multi-scale simulations require parallelization to address large-scale problems, such as real-sized tumor simulations. BioFVM is a software package that solves diffusive transport Partial Differential Equations for 3-D biological simulations successfully applied to tissue and cancer biology problems. Currently, BioFVM is only shared-memory parallelized using OpenMP, greatly limiting the execution of large-scale jobs in HPC clusters. We present BioFVM-X: an enhanced version of BioFVM capable of running on multiple nodes. BioFVM-X uses MPI+OpenMP to parallelize the generic core kernels of BioFVM and shows promising scalability in large 3-D problems with several hundreds diffusible substrates and ≈ 0.5 billion voxels. The BioFVM-X source code, examples and documentation, are available under the BSD 3-Clause license at https://gitlab.bsc.es/gsaxena/biofvm_x.The research leading to these results has received funding from EU H2020 Programme under the PerMedCoE project, grant agreement number 951773 and the INFORE project, grant agreement number 825070. The authors would like to thank Paul Macklin and Randy Heiland from Indiana University for their constant support and advice regarding BioFVM.Peer ReviewedPostprint (published version