BioFVM-X

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 (approx 0.5) billion voxels. The BioFVM-X source code, examples and documentation, are available under the BSD 3-Clause license at url{https://gitlab.bsc.es/gsaxena/biofvm_x}.

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